[ { "id": "Q1KMD3-1.161.161", "start_pos": 161, "end_pos": 161, "uniprot_canonical_ac": "Q1KMD3-1", "length": 747, "uniprot_id": "HNRL2_HUMAN", "protein_name": "Heterogeneous nuclear ribonucleoprotein U-like protein 2", "refseq_ac": "NP_001073027", "refseq_name": "heterogeneous nuclear ribonucleoprotein U-like protein 2", "gene_name": "HNRNPUL2", "gene_names_uniprotkb": "HNRNPUL2; HNRPUL2", "gene_names_refseq": "HNRNPUL2; HNRPUL2; SAF-A2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "title": "Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008", "authors": "McNulty DE, Annan RS", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Phosphoproteomic analysis of human brain by calcium phosphate precipitation and mass spectrometry.", "journal": "Journal of proteome research", "date": "2008", "authors": "Xia Q, Cheng D, Duong DM, Gearing M, Lah JJ, Levey AI, Peng J", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355" } ] }, { "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": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Molecular cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Immobilized metal affinity chromatography revisited: pH/acid control toward high selectivity in phosphoproteomics.", "journal": "Journal of proteome research", "date": "2008", "authors": "Tsai CF, Wang YT, Chen YR, Lai CY, Lin PY, Pan KT, Chen JY, Khoo KH, Chen YJ", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" } ] }, { "title": "Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis.", "journal": "Analytical chemistry", "date": "2008", "authors": "Wang B, Malik R, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "title": "Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer.", "journal": "Analytical chemistry", "date": "2010", "authors": "Raijmakers R, Kraiczek K, de Jong AP, Mohammed S, Heck AJ", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] }, { "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "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": "VNGGEEQGLGKREEDEPEER", "down_seq": "GDETPGSEVPGDKAAEEQGD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" }, { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" }, { "database": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser161" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "691", "end_pos": "691" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q1KMD3-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q1KMD3-1.165.165", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q1KMD3-1.168.168", "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": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q1KMD3-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "Q1KMD3-1", "length": 747, "uniprot_id": "HNRL2_HUMAN", "protein_name": "Heterogeneous nuclear ribonucleoprotein U-like protein 2", "refseq_ac": "NP_001073027", "refseq_name": "heterogeneous nuclear ribonucleoprotein U-like protein 2", "gene_name": "HNRNPUL2", "gene_names_uniprotkb": "HNRNPUL2; HNRPUL2", "gene_names_refseq": "HNRNPUL2; HNRPUL2; SAF-A2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" } ], "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": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "T", "start_aa": "T", "up_seq": "EEQGLGKREEDEPEERSGDE", "down_seq": "PGSEVPGDKAAEEQGDDQDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" }, { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr165" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "691", "end_pos": "691" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q1KMD3-1.161.161", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q1KMD3-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q1KMD3-1.168.168", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q1KMD3-1.185.185", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q1KMD3-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "Q1KMD3-1", "length": 747, "uniprot_id": "HNRL2_HUMAN", "protein_name": "Heterogeneous nuclear ribonucleoprotein U-like protein 2", "refseq_ac": "NP_001073027", "refseq_name": "heterogeneous nuclear ribonucleoprotein U-like protein 2", "gene_name": "HNRNPUL2", "gene_names_uniprotkb": "HNRNPUL2; HNRPUL2", "gene_names_refseq": "HNRNPUL2; HNRPUL2; SAF-A2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" } ], "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": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GLGKREEDEPEERSGDETPG", "down_seq": "EVPGDKAAEEQGDDQDSEKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" }, { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser168" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "691", "end_pos": "691" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q1KMD3-1.161.161", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q1KMD3-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q1KMD3-1.165.165", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q1KMD3-1.185.185", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q1KMD3-1.188.188", "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": "Q1KMD3-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "Q1KMD3-1", "length": 747, "uniprot_id": "HNRL2_HUMAN", "protein_name": "Heterogeneous nuclear ribonucleoprotein U-like protein 2", "refseq_ac": "NP_001073027", "refseq_name": "heterogeneous nuclear ribonucleoprotein U-like protein 2", "gene_name": "HNRNPUL2", "gene_names_uniprotkb": "HNRNPUL2; HNRPUL2", "gene_names_refseq": "HNRNPUL2; HNRPUL2; SAF-A2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" } ], "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3", "database": "iPTMnet", "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": "TPGSEVPGDKAAEEQGDDQD", "down_seq": "EKSKPAGSDGERRGVKRQRD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" }, { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser185" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "691", "end_pos": "691" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q1KMD3-1.165.165", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q1KMD3-1.168.168", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q1KMD3-1.188.188", "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": "Q1KMD3-1.188.188", "start_pos": 188, "end_pos": 188, "uniprot_canonical_ac": "Q1KMD3-1", "length": 747, "uniprot_id": "HNRL2_HUMAN", "protein_name": "Heterogeneous nuclear ribonucleoprotein U-like protein 2", "refseq_ac": "NP_001073027", "refseq_name": "heterogeneous nuclear ribonucleoprotein U-like protein 2", "gene_name": "HNRNPUL2", "gene_names_uniprotkb": "HNRNPUL2; HNRPUL2", "gene_names_refseq": "HNRNPUL2; HNRPUL2; SAF-A2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SEVPGDKAAEEQGDDQDSEK", "down_seq": "KPAGSDGERRGVKRQRDEKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" } ], "site_lbl": "Ser188" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "691", "end_pos": "691" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q1KMD3-1.168.168", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q1KMD3-1.185.185", "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": "Q1KMD3-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "Q1KMD3-1", "length": 747, "uniprot_id": "HNRL2_HUMAN", "protein_name": "Heterogeneous nuclear ribonucleoprotein U-like protein 2", "refseq_ac": "NP_001073027", "refseq_name": "heterogeneous nuclear ribonucleoprotein U-like protein 2", "gene_name": "HNRNPUL2", "gene_names_uniprotkb": "HNRNPUL2; HNRPUL2", "gene_names_refseq": "HNRNPUL2; HNRPUL2; SAF-A2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" } ], "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Molecular cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "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": "EKDEHGRAYYEFREEAYHSR", "down_seq": "KSPLPPEEEAKDEEEDQTLV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" }, { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser226" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "691", "end_pos": "691" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q1KMD3-1.228.228", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q1KMD3-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "Q1KMD3-1", "length": 747, "uniprot_id": "HNRL2_HUMAN", "protein_name": "Heterogeneous nuclear ribonucleoprotein U-like protein 2", "refseq_ac": "NP_001073027", "refseq_name": "heterogeneous nuclear ribonucleoprotein U-like protein 2", "gene_name": "HNRNPUL2", "gene_names_uniprotkb": "HNRNPUL2; HNRPUL2", "gene_names_refseq": "HNRNPUL2; HNRPUL2; SAF-A2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" } ], "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Phosphoproteomic analysis of human brain by calcium phosphate precipitation and mass spectrometry.", "journal": "Journal of proteome research", "date": "2008", "authors": "Xia Q, Cheng D, Duong DM, Gearing M, Lah JJ, Levey AI, Peng J", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355" } ] }, { "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": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Molecular cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "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": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "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": "DEHGRAYYEFREEAYHSRSK", "down_seq": "PLPPEEEAKDEEEDQTLVNL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q1KMD3", "url": "https://www.uniprot.org/uniprotkb/Q1KMD3" }, { "database": "iPTMnet", "id": "Q1KMD3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q1KMD3" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser228" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "299", "end_pos": "299" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "671", "end_pos": "671" }, { "start_pos": "691", "end_pos": "691" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q1KMD3-1.226.226", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5VY09-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "Q5VY09-1", "length": 327, "uniprot_id": "IER5_HUMAN", "protein_name": "Immediate early response gene 5 protein", "refseq_ac": "NP_057629", "refseq_name": "immediate early response gene 5 protein", "gene_name": "IER5", "gene_names_uniprotkb": "IER5; PP4583; SBBI48", "gene_names_refseq": "IER5; SBBI48", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VY09", "url": "https://www.uniprot.org/uniprotkb/Q5VY09" } ], "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": "rs891378577", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs891378577", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs891378577", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs891378577", "database": "1000Genomes", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ARQVYLSDPCPGLYLAGPAG", "down_seq": "PAPPPQQQPGEPAAGPPAGW", "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": "Thr63", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs891378577", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs891378577" }, { "id": "rs891378577", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs891378577" } ], "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": "181089090", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T63", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs891378577", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs891378577" }, { "id": "rs891378577", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs891378577" } ], "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": "1", "chr_pos": "181089090", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T63", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "92", "end_pos": "92" } ] } ], "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" ] }, { "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": "Q5VY09-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "Q5VY09-1", "length": 327, "uniprot_id": "IER5_HUMAN", "protein_name": "Immediate early response gene 5 protein", "refseq_ac": "NP_057629", "refseq_name": "immediate early response gene 5 protein", "gene_name": "IER5", "gene_names_uniprotkb": "IER5; PP4583; SBBI48", "gene_names_refseq": "IER5; SBBI48", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VY09", "url": "https://www.uniprot.org/uniprotkb/Q5VY09" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VY09", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VY09", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MEFKLEAHRIV", "down_seq": "ISLGKIYNSRVQRGGIKLHK", "snv": [ { "evidence": [ { "id": "Q5VY09", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VY09" } ], "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 (SIS->NIS).", "chr_id": "1", "chr_pos": "181088937", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S12", "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": "63", "end_pos": "63" } ] }, { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "63", "end_pos": "63" }, { "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": "Q5VY09-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "Q5VY09-1", "length": 327, "uniprot_id": "IER5_HUMAN", "protein_name": "Immediate early response gene 5 protein", "refseq_ac": "NP_057629", "refseq_name": "immediate early response gene 5 protein", "gene_name": "IER5", "gene_names_uniprotkb": "IER5; PP4583; SBBI48", "gene_names_refseq": "IER5; SBBI48", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VY09", "url": "https://www.uniprot.org/uniprotkb/Q5VY09" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1242405400", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1242405400", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1242405400", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1242405400#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1242405400", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1242405400", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DEVPVATVTGVGDVFQGGEA", "down_seq": "ATEAAWSRVEGPRQAAAREA", "snv": [ { "evidence": [ { "id": "rs1242405400", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1242405400" }, { "id": "rs1242405400", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1242405400#frequency_tab" }, { "id": "rs1242405400", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1242405400" } ], "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": "1", "chr_pos": "181089305", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D135", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "63", "end_pos": "63" }, { "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5VY09-1.267.267", "start_pos": 267, "end_pos": 267, "uniprot_canonical_ac": "Q5VY09-1", "length": 327, "uniprot_id": "IER5_HUMAN", "protein_name": "Immediate early response gene 5 protein", "refseq_ac": "NP_057629", "refseq_name": "immediate early response gene 5 protein", "gene_name": "IER5", "gene_names_uniprotkb": "IER5; PP4583; SBBI48", "gene_names_refseq": "IER5; SBBI48", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VY09", "url": "https://www.uniprot.org/uniprotkb/Q5VY09" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs376566028", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376566028", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs376566028", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376566028#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs376566028", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376566028", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EQPPSGGEDDDAEEMETGNV", "down_seq": "NLISIFGSSFSGLLRKSPGG", "snv": [ { "evidence": [ { "id": "rs376566028", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376566028" }, { "id": "rs376566028", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376566028#frequency_tab" }, { "id": "rs376566028", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376566028" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVA->NVT).", "chr_id": "1", "chr_pos": "181089701", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A267", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "63", "end_pos": "63" }, { "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5VY09-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "Q5VY09-1", "length": 327, "uniprot_id": "IER5_HUMAN", "protein_name": "Immediate early response gene 5 protein", "refseq_ac": "NP_057629", "refseq_name": "immediate early response gene 5 protein", "gene_name": "IER5", "gene_names_uniprotkb": "IER5; PP4583; SBBI48", "gene_names_refseq": "IER5; SBBI48", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VY09", "url": "https://www.uniprot.org/uniprotkb/Q5VY09" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VY09", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VY09", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PGEPAAGPPAGWGEPPPPAA", "down_seq": "ASWPETEPQPERSSVSDAPR", "snv": [ { "evidence": [ { "id": "Q5VY09", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VY09" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "3", "frequency": "3.3", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: patient freq. (3.3%).", "chr_id": "1", "chr_pos": "181089177", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R92", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "63", "end_pos": "63" }, { "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": 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": "Q6ZVW7-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "Q6ZVW7-1", "length": 507, "uniprot_id": "I17EL_HUMAN", "protein_name": "Interleukin-17 receptor E-like protein", "refseq_ac": "NP_001001694", "refseq_name": "interleukin-17 receptor E-like protein isoform 1", "gene_name": "IL17REL", "gene_names_uniprotkb": "IL17REL", "gene_names_refseq": "IL17REL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZVW7", "url": "https://www.uniprot.org/uniprotkb/Q6ZVW7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZVW7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZVW7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TLHERLRGLEACAMSLDTQE", "down_seq": "QCQSVWVARASHRQQGGQQL", "snv": [ { "evidence": [ { "id": "Q6ZVW7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZVW7" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "50000812", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T111", "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: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" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "81", "end_pos": "81" } ] } ], "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": "Q6ZVW7-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "Q6ZVW7-1", "length": 507, "uniprot_id": "I17EL_HUMAN", "protein_name": "Interleukin-17 receptor E-like protein", "refseq_ac": "NP_001001694", "refseq_name": "interleukin-17 receptor E-like protein isoform 1", "gene_name": "IL17REL", "gene_names_uniprotkb": "IL17REL", "gene_names_refseq": "IL17REL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZVW7", "url": "https://www.uniprot.org/uniprotkb/Q6ZVW7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZVW7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZVW7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SVLEALTSSTAMQCVPSDGC", "down_seq": "MLLRVRASITLHERLRGLEA", "snv": [ { "evidence": [ { "id": "Q6ZVW7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZVW7" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "50001120", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A81", "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: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": "111", "end_pos": "111" }, { "start_pos": "81", "end_pos": "81" } ] } ], "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": "Q7Z5L9-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1334847747", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1334847747", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1334847747", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1334847747#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1334847747", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1334847747", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AAAERPPRLGSDFGSSRPAA", "down_seq": "LAQPPTPQPPPVNGILVPNG", "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": "Ser141", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1334847747", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1334847747" }, { "id": "rs1334847747", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1334847747#frequency_tab" }, { "id": "rs1334847747", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1334847747" } ], "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": "1", "chr_pos": "234609073", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S141", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q7Z5L9-1.147.147", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1672264477", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672264477", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1672264477", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672264477#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1672264436", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672264436", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1672264436", "url": "https://www.ensembl.org/id/rs1672264436", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PRLGSDFGSSRPAASLAQPP", "down_seq": "PQPPPVNGILVPNGFSKLEE", "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": "Thr147", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1672264477", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672264477" }, { "id": "rs1672264477", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672264477#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": "1", "chr_pos": "234609056", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T147", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1672264436", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672264436" } ], "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": "1", "chr_pos": "234609055", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T147", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1672264436", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672264436" }, { "id": "rs1672264436", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1672264436" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "1", "chr_pos": "234609055", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T147", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1672264477", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672264477" }, { "id": "rs1672264477", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672264477#frequency_tab" } ], "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": "234609056", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T147", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q7Z5L9-1.141.141", "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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.212.212", "start_pos": 212, "end_pos": 212, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.", "journal": "Molecular cell", "date": "2023-08-17", "authors": "Xu Chenchen, Pan Xiaoqing, Wang Dong, Guan Yuanyuan, Yang Wenyu, Chen Xing, Liu Ying", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] }, { "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": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1359057627", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1359057627", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1359057627", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1359057627#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1359057627", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1359057627", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1048225903", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1048225903", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1048225903", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1048225903#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1048225903", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1048225903", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MNGSATPLPTALGLGGRAAA", "down_seq": "LAAVSGTAAASLGSAQPTDL", "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": "Ser212", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" }, { "id": "32938750", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32938750" } ] } ], "snv": [ { "evidence": [ { "id": "rs1359057627", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1359057627" }, { "id": "rs1359057627", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1359057627#frequency_tab" }, { "id": "rs1359057627", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1359057627" } ], "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": "1", "chr_pos": "234608861", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S212", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1048225903", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1048225903" }, { "id": "rs1048225903", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1048225903#frequency_tab" }, { "id": "rs1048225903", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1048225903" } ], "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": "1", "chr_pos": "234608860", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S212", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1048225903", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1048225903" }, { "id": "rs1048225903", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1048225903#frequency_tab" }, { "id": "rs1048225903", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1048225903" } ], "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": "1", "chr_pos": "234608860", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S212", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q7Z5L9-1.195.195", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7Z5L9-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5L9-1.219.219", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7Z5L9-1.223.223", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z5L9-1.226.226", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q7Z5L9-1.230.230", "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": 22 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.", "journal": "Molecular cell", "date": "2023-08-17", "authors": "Xu Chenchen, Pan Xiaoqing, Wang Dong, Guan Yuanyuan, Yang Wenyu, Chen Xing, Liu Ying", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] }, { "title": "Cell-type-specific labeling and profiling of glycans in living mice.", "journal": "Nature chemical biology", "date": "2022-06", "authors": "Fan Xinqi, Song Qitao, Sun De-En, Hao Yi, Wang Jingyang, Wang Chunting, Chen Xing", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs2528520886", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2528520886", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1672253389", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672253389", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1672253389", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672253389#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1672253389", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1672253389", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5L9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPLPTALGLGGRAAASLAAV", "down_seq": "GTAAASLGSAQPTDLGAHKR", "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": "Ser217", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "id": "35513511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35513511" } ] }, { "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": "Ser217", "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": "rs2528520886", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2528520886" } ], "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": "1", "chr_pos": "234608845", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1672253389", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672253389" }, { "id": "rs1672253389", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672253389#frequency_tab" }, { "id": "rs1672253389", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1672253389" } ], "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": "1", "chr_pos": "234608846", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q7Z5L9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5L9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4484", "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": "1", "chr_pos": "234608845", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S217", "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": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q7Z5L9-1.212.212", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5L9-1.219.219", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q7Z5L9-1.223.223", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q7Z5L9-1.226.226", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q7Z5L9-1.230.230", "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": 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": 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": 22 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.219.219", "start_pos": 219, "end_pos": 219, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1672253184", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672253184", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1672253184", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672253184#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1672253184", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1672253184", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5L9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2102769665", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102769665", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102769665", "url": "https://www.ensembl.org/id/rs2102769665", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LPTALGLGGRAAASLAAVSG", "down_seq": "AAASLGSAQPTDLGAHKRPA", "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": "Thr219", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1672253184", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672253184" }, { "id": "rs1672253184", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672253184#frequency_tab" }, { "id": "rs1672253184", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1672253184" } ], "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": "234608839", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T219", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1672253184", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672253184" }, { "id": "rs1672253184", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672253184#frequency_tab" }, { "id": "rs1672253184", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1672253184" } ], "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": "1", "chr_pos": "234608839", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T219", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q7Z5L9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5L9" }, { "id": "rs2102769665", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102769665" }, { "id": "rs2102769665", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102769665" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "8", "frequency": "0.3", "sequence_org": "T", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "1", "chr_pos": "234608840", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "T219", "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": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q7Z5L9-1.212.212", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5L9-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5L9-1.223.223", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5L9-1.226.226", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7Z5L9-1.230.230", "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", "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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins.", "journal": "Cell reports", "date": "2022-06-14", "authors": "Xu Senhan, Tong Ming, Suttapitugsakul Suttipong, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] }, { "title": "OGA mutant aberrantly hydrolyzes O-GlcNAc modification from PDLIM7 to modulate p53 and cytoskeleton in promoting cancer cell malignancy.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-06-11", "authors": "Hu Chia-Wei, Wang Ao, Fan Dacheng, Worth Matthew, Chen Zhengwei, Huang Junfeng, Xie Jinshan, Macdonald John, Li Lingjun, Jiang Jiaoyang", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1308873079", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1308873079", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1308873079", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1308873079", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1310046018", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1310046018", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1310046018", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1310046018#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1310046018", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1310046018", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGLGGRAAASLAAVSGTAAA", "down_seq": "LGSAQPTDLGAHKRPASVSS", "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": "Ser223", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "id": "38838015", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38838015" } ] } ], "snv": [ { "evidence": [ { "id": "rs1308873079", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1308873079" }, { "id": "rs1308873079", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1308873079" } ], "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": "1", "chr_pos": "234608828", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S223", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1310046018", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1310046018" }, { "id": "rs1310046018", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1310046018#frequency_tab" }, { "id": "rs1310046018", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1310046018" } ], "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": "1", "chr_pos": "234608827", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S223", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q7Z5L9-1.212.212", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q7Z5L9-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5L9-1.219.219", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5L9-1.226.226", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5L9-1.230.230", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q7Z5L9-1.240.240", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q7Z5L9-1.242.242", "categories": [ "glycosylation_flag", "snv_flag", "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": 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": 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": 22 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1389085714", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1389085714", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1389085714", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1389085714", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1389085714", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1389085714", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2102769633", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102769633", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102769633", "url": "https://www.ensembl.org/id/rs2102769633", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GGRAAASLAAVSGTAAASLG", "down_seq": "AQPTDLGAHKRPASVSSSAA", "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": "Ser226", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1389085714", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1389085714" }, { "id": "rs1389085714", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1389085714" }, { "id": "rs1389085714", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1389085714" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "1", "chr_pos": "234608818", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S226", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs2102769633", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102769633" }, { "id": "rs2102769633", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102769633" } ], "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": "1", "chr_pos": "234608819", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S226", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q7Z5L9-1.212.212", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q7Z5L9-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5L9-1.219.219", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5L9-1.223.223", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5L9-1.230.230", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z5L9-1.240.240", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q7Z5L9-1.242.242", "categories": [ "glycosylation_flag", "snv_flag", "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": 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": 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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.230.230", "start_pos": 230, "end_pos": 230, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1363709762", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1363709762", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1363709762", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1363709762#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1363709762", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1363709762", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1672251085", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672251085", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1672251085", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672251085#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AASLAAVSGTAAASLGSAQP", "down_seq": "DLGAHKRPASVSSSAAVEHE", "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": "Thr230", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1363709762", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1363709762" }, { "id": "rs1363709762", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1363709762#frequency_tab" }, { "id": "rs1363709762", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1363709762" } ], "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": "1", "chr_pos": "234608807", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T230", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1672251085", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672251085" }, { "id": "rs1672251085", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672251085#frequency_tab" } ], "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": "234608806", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T230", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q7Z5L9-1.212.212", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q7Z5L9-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q7Z5L9-1.219.219", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5L9-1.223.223", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5L9-1.226.226", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5L9-1.240.240", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q7Z5L9-1.242.242", "categories": [ "glycosylation_flag", "snv_flag", "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": 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": 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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "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": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs771536127", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771536127", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771536127", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771536127#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771536127", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771536127", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AAASLGSAQPTDLGAHKRPA", "down_seq": "VSSSAAVEHEQREAAAKEKQ", "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": "Ser240", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs771536127", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771536127" }, { "id": "rs771536127", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771536127#frequency_tab" }, { "id": "rs771536127", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771536127" } ], "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": "1", "chr_pos": "234608776", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S240", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771536127", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771536127" } ], "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": "1", "chr_pos": "234608776", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S240", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser240" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q7Z5L9-1.223.223", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q7Z5L9-1.226.226", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q7Z5L9-1.230.230", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5L9-1.242.242", "categories": [ "glycosylation_flag", "snv_flag", "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": 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": 26 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1292572073", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1292572073", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1292572073", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1292572073#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1292572073", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1292572073", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASLGSAQPTDLGAHKRPASV", "down_seq": "SSAAVEHEQREAAAKEKQPP", "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": "Ser242", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "id": "32938750", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32938750" } ] } ], "snv": [ { "evidence": [ { "id": "rs1292572073", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1292572073" }, { "id": "rs1292572073", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1292572073#frequency_tab" }, { "id": "rs1292572073", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1292572073" } ], "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": "1", "chr_pos": "234608771", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S242", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser242" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q7Z5L9-1.223.223", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q7Z5L9-1.226.226", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q7Z5L9-1.230.230", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5L9-1.240.240", "categories": [ "glycosylation_flag", "snv_flag", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 22 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.381.381", "start_pos": 381, "end_pos": 381, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1672205059", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672205059", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1672205059", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672205059#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1672205059", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1672205059", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "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": "PEPEGEVGPPKINGEAQPWL", "down_seq": "TSTEGLKIPMTPTSSFVSPP", "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": "Ser381", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1672205059", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672205059" }, { "id": "rs1672205059", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672205059#frequency_tab" }, { "id": "rs1672205059", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1672205059" } ], "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": "1", "chr_pos": "234607759", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S381", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser381" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q7Z5L9-1.382.382", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5L9-1.383.383", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5L9-1.384.384", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q7Z5L9-1.399.399", "categories": [ "glycosylation_flag", "snv_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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 21 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.382.382", "start_pos": 382, "end_pos": 382, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1242839412", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1242839412", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1242839412", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1242839412", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1361153187", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1361153187", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1361153187", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1361153187", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EPEGEVGPPKINGEAQPWLS", "down_seq": "STEGLKIPMTPTSSFVSPPP", "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": "Thr382", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1242839412", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1242839412" }, { "id": "rs1242839412", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1242839412" } ], "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": "1", "chr_pos": "234607757", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T382", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1361153187", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1361153187" }, { "id": "rs1361153187", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1361153187" } ], "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": "234607756", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T382", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q7Z5L9-1.381.381", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5L9-1.383.383", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5L9-1.384.384", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q7Z5L9-1.399.399", "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": 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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.383.383", "start_pos": 383, "end_pos": 383, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.", "journal": "Molecular cell", "date": "2023-08-17", "authors": "Xu Chenchen, Pan Xiaoqing, Wang Dong, Guan Yuanyuan, Yang Wenyu, Chen Xing, Liu Ying", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] }, { "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": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] }, { "title": "Cell-type-specific labeling and profiling of glycans in living mice.", "journal": "Nature chemical biology", "date": "2022-06", "authors": "Fan Xinqi, Song Qitao, Sun De-En, Hao Yi, Wang Jingyang, Wang Chunting, Chen Xing", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511" } ] }, { "title": "Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins.", "journal": "Cell reports", "date": "2022-06-14", "authors": "Xu Senhan, Tong Ming, Suttapitugsakul Suttipong, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142", "database": "Data Submission", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PEGEVGPPKINGEAQPWLST", "down_seq": "TEGLKIPMTPTSSFVSPPPP", "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": "Ser383", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "id": "32938750", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32938750" }, { "id": "35513511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35513511" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" } ] }, { "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": "Ser383", "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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q7Z5L9-1.381.381", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5L9-1.382.382", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5L9-1.384.384", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q7Z5L9-1.399.399", "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": 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": 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": 24 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.384.384", "start_pos": 384, "end_pos": 384, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] } ], "crossref": [ { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1672202587", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672202587", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1672202587", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672202587#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EGEVGPPKINGEAQPWLSTS", "down_seq": "EGLKIPMTPTSSFVSPPPPT", "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": "Thr384", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1672202587", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672202587" }, { "id": "rs1672202587", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672202587#frequency_tab" } ], "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": "234607750", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T384", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q7Z5L9-1.381.381", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5L9-1.382.382", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5L9-1.383.383", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q7Z5L9-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q7Z5L9-1.404.404", "categories": [ "glycosylation_flag", "snv_flag", "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": 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": "Q7Z5L9-1.392.392", "start_pos": 392, "end_pos": 392, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies.", "journal": "Molecular immunology", "date": "2020-07", "authors": "Pandey Kirti, Mifsud Nicole A, Lim Kam Sian Terry C C, Ayala Rochelle, Ternette Nicola, Ramarathinam Sri H, Purcell Anthony W", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "IEDB", "id": "437472", "url": "https://www.iedb.org/epitope/437472" }, { "database": "IEDB", "id": "445176", "url": "https://www.iedb.org/epitope/445176" }, { "database": "IEDB", "id": "453936", "url": "https://www.iedb.org/epitope/453936" }, { "database": "IEDB", "id": "454766", "url": "https://www.iedb.org/epitope/454766" }, { "database": "IEDB", "id": "1348084", "url": "https://www.iedb.org/epitope/1348084" }, { "database": "IEDB", "id": "1348512", "url": "https://www.iedb.org/epitope/1348512" }, { "database": "IEDB", "id": "1356581", "url": "https://www.iedb.org/epitope/1356581" }, { "database": "IEDB", "id": "1366309", "url": "https://www.iedb.org/epitope/1366309" }, { "database": "IEDB", "id": "1374449", "url": "https://www.iedb.org/epitope/1374449" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1571957075", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571957075", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1571957075", "url": "https://www.ensembl.org/id/rs1571957075", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.iedb.org/epitope/Q7Z5L9", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "INGEAQPWLSTSTEGLKIPM", "down_seq": "PTSSFVSPPPPTASPHSNRT", "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": "Thr392", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1571957075", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571957075" }, { "id": "rs1571957075", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1571957075" } ], "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": "234607727", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T392", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q7Z5L9", "url": "https://www.iedb.org/epitope/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ], "site_lbl": "Thr392" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q7Z5L9-1.381.381", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q7Z5L9-1.382.382", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q7Z5L9-1.383.383", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q7Z5L9-1.384.384", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5L9-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q7Z5L9-1.404.404", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z5L9-1.406.406", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q7Z5L9-1.409.409", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q7Z5L9-1.412.412", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 21 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.395.395", "start_pos": 395, "end_pos": 395, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] }, { "title": "Cell-type-specific labeling and profiling of glycans in living mice.", "journal": "Nature chemical biology", "date": "2022-06", "authors": "Fan Xinqi, Song Qitao, Sun De-En, Hao Yi, Wang Jingyang, Wang Chunting, Chen Xing", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EAQPWLSTSTEGLKIPMTPT", "down_seq": "SFVSPPPPTASPHSNRTTPP", "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": "Ser395", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "id": "32938750", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32938750" }, { "id": "35513511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35513511" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q7Z5L9-1.381.381", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q7Z5L9-1.382.382", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q7Z5L9-1.383.383", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q7Z5L9-1.384.384", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5L9-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q7Z5L9-1.404.404", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7Z5L9-1.406.406", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z5L9-1.409.409", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q7Z5L9-1.412.412", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q7Z5L9-1.413.413", "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": 22 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.396.396", "start_pos": 396, "end_pos": 396, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "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": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1672201308", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672201308", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1672201308", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672201308#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AQPWLSTSTEGLKIPMTPTS", "down_seq": "FVSPPPPTASPHSNRTTPPE", "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": "Ser396", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1672201308", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672201308" }, { "id": "rs1672201308", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672201308#frequency_tab" } ], "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": "1", "chr_pos": "234607714", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S396", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser396" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q7Z5L9-1.381.381", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q7Z5L9-1.382.382", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q7Z5L9-1.383.383", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q7Z5L9-1.384.384", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5L9-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q7Z5L9-1.404.404", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5L9-1.406.406", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q7Z5L9-1.409.409", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q7Z5L9-1.412.412", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q7Z5L9-1.413.413", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q7Z5L9-1.399.399", "start_pos": 399, "end_pos": 399, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" }, { "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": "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1672201162", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672201162", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1672201162", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672201162#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WLSTSTEGLKIPMTPTSSFV", "down_seq": "PPPPTASPHSNRTTPPEAAQ", "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": "Ser399", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1672201162", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672201162" }, { "id": "rs1672201162", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1672201162#frequency_tab" } ], "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": "1", "chr_pos": "234607705", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S399", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q7Z5L9-1.381.381", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q7Z5L9-1.382.382", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q7Z5L9-1.383.383", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q7Z5L9-1.384.384", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7Z5L9-1.404.404", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5L9-1.406.406", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5L9-1.409.409", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q7Z5L9-1.412.412", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z5L9-1.413.413", "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": 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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.404.404", "start_pos": 404, "end_pos": 404, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1672200261", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672200261", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755960984", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755960984", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755960984", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755960984", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755960984", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755960984#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs755960984", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755960984", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "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": "TEGLKIPMTPTSSFVSPPPP", "down_seq": "ASPHSNRTTPPEAAQNGQSP", "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": "Thr404", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1672200261", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1672200261" } ], "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": "234607690", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T404", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs755960984", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755960984" }, { "id": "rs755960984", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755960984" }, { "id": "rs755960984", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755960984#frequency_tab" }, { "id": "rs755960984", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755960984" } ], "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": "234607691", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T404", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr404" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q7Z5L9-1.384.384", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q7Z5L9-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5L9-1.406.406", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7Z5L9-1.409.409", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q7Z5L9-1.412.412", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q7Z5L9-1.413.413", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q7Z5L9-1.423.423", "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": 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": 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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "Q7Z5L9-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z5L9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z5L9" }, { "database": "O-GlcNAc Atlas", "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] } ], "crossref": [ { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IPMTPTSSFVSPPPPTASPH", "down_seq": "NRTTPPEAAQNGQSPMAALI", "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": "Ser409", "evidence": [ { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "Q7Z5L9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q7Z5L9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q7Z5L9-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q7Z5L9-1.404.404", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5L9-1.406.406", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5L9-1.412.412", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5L9-1.413.413", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z5L9-1.423.423", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "rs781552801", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781552801", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781552801", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781552801", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781552801", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781552801#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs781552801", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781552801", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "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": "REAAAKEKQPPPPAHRGPAD", "down_seq": "LSTAAGAAELSAEGAGKSRG", "snv": [ { "evidence": [ { "id": "rs781552801", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781552801" }, { "id": "rs781552801", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781552801" }, { "id": "rs781552801", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781552801#frequency_tab" }, { "id": "rs781552801", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781552801" } ], "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": "1", "chr_pos": "234608680", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S272", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser272" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q7Z5L9-1.302.302", "start_pos": 302, "end_pos": 302, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771825886", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771825886", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771825886", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771825886", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771825886", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771825886#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771825886", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771825886", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs771825886", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771825886", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LSAEGAGKSRGSGEQDWVNR", "down_seq": "KTVRDTLLALHQHGHSGPFE", "snv": [ { "evidence": [ { "id": "rs771825886", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771825886" }, { "id": "rs771825886", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771825886" }, { "id": "rs771825886", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771825886#frequency_tab" }, { "id": "rs771825886", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771825886" }, { "id": "rs771825886", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771825886" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NRP->NRS).", "chr_id": "1", "chr_pos": "234608591", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P302", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q7Z5L9-1.318.318", "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": "Q7Z5L9-1.448.448", "start_pos": 448, "end_pos": 448, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1455810393", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1455810393", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1455810393", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1455810393#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1455810393", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1455810393", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LILVADNAGGSHASKDANQV", "down_seq": "STTRRNSNSPPSPSSMNQRR", "snv": [ { "evidence": [ { "id": "rs1455810393", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1455810393" }, { "id": "rs1455810393", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1455810393#frequency_tab" }, { "id": "rs1455810393", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1455810393" } ], "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": "1", "chr_pos": "234607559", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H448", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q7Z5L9-1.455.455", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q7Z5L9-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q7Z5L9-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5L9-1.458.458", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q7Z5L9-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z5L9-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q7Z5L9-1.463.463", "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": "Q7Z5L9-1.455.455", "start_pos": 455, "end_pos": 455, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "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": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "rs780856249", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780856249", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780856249", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780856249", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780856249", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780856249", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "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": "AGGSHASKDANQVHSTTRRN", "down_seq": "NSPPSPSSMNQRRLGPREVG", "snv": [ { "evidence": [ { "id": "rs780856249", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780856249" }, { "id": "rs780856249", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780856249" }, { "id": "rs780856249", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780856249" } ], "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 (SNS->NNS).", "chr_id": "1", "chr_pos": "234607537", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S455", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser455" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q7Z5L9-1.448.448", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5L9-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5L9-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5L9-1.458.458", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7Z5L9-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5L9-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q7Z5L9-1.463.463", "categories": [ "phosphorylation_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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q7Z5L9-1.456.456", "start_pos": 456, "end_pos": 456, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs933341421", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs933341421", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs933341421", "url": "https://www.ncbi.nlm.nih.gov/snp/rs933341421#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GGSHASKDANQVHSTTRRNS", "down_seq": "SPPSPSSMNQRRLGPREVGG", "snv": [ { "evidence": [ { "id": "rs933341421", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs933341421" }, { "id": "rs933341421", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs933341421#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSN->NSS).", "chr_id": "1", "chr_pos": "234607534", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N456", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q7Z5L9-1.448.448", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5L9-1.455.455", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5L9-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5L9-1.458.458", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5L9-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q7Z5L9-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5L9-1.463.463", "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": "Q7Z5L9-1.458.458", "start_pos": 458, "end_pos": 458, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z5L9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5L9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs780007094", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780007094", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780007094", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780007094", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780007094", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780007094", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs780007094", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs780007094", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SHASKDANQVHSTTRRNSNS", "down_seq": "PSPSSMNQRRLGPREVGGQG", "snv": [ { "evidence": [ { "id": "Q7Z5L9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5L9" }, { "id": "rs780007094", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780007094" }, { "id": "rs780007094", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780007094" }, { "id": "rs780007094", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780007094" }, { "id": "rs780007094", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs780007094" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSP->NSS).", "chr_id": "1", "chr_pos": "234607529", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P458", "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: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": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q7Z5L9-1.448.448", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5L9-1.455.455", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5L9-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5L9-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5L9-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q7Z5L9-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7Z5L9-1.463.463", "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": "Q7Z5L9-1.495.495", "start_pos": 495, "end_pos": 495, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z5L9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5L9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GGQGAGNTGGLEPVHPASLP", "down_seq": "SSLATSAPLCCTLCHERLED", "snv": [ { "evidence": [ { "id": "Q7Z5L9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5L9" } ], "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 (DSS->NSS).", "chr_id": "1", "chr_pos": "234607418", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D495", "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": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "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": "Q7Z5L9-1.528.528", "start_pos": 528, "end_pos": 528, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746374377", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746374377", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746374377", "url": "https://www.ensembl.org/id/rs746374377", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LCHERLEDTHFVQCPSVPSH", "down_seq": "FCFPCSRQSIKQQGASGEVY", "snv": [ { "evidence": [ { "id": "rs746374377", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746374377" }, { "id": "rs746374377", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs746374377" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KFC->NFC).", "chr_id": "1", "chr_pos": "234607317", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K528", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "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": "Q7Z5L9-1.563.563", "start_pos": 563, "end_pos": 563, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs916648659", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs916648659", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs916648659", "url": "https://www.ncbi.nlm.nih.gov/snp/rs916648659#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs916648659", "url": "http://gnomad.broadinstitute.org/awesome?query=rs916648659", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ASGEVYCPSGEKCPLVGSNV", "down_seq": "WAFMQGEIATILAGDVKVKK", "snv": [ { "evidence": [ { "id": "rs916648659", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs916648659" }, { "id": "rs916648659", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs916648659#frequency_tab" }, { "id": "rs916648659", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs916648659" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVP->NVS).", "chr_id": "1", "chr_pos": "234607214", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P563", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs916648659", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs916648659" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVP->NVT).", "chr_id": "1", "chr_pos": "234607214", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P563", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "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": "Q7Z5L9-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z5L9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5L9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLKRAHGCFPEGRSPPGAAA", "down_seq": "AAAKPPPLSAKDILLQQQQQ", "snv": [ { "evidence": [ { "id": "Q7Z5L9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z5L9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "2", "frequency": "2.2", "sequence_org": "S", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: patient freq. (2.2%).", "chr_id": "1", "chr_pos": "234609263", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S78", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q7Z5L9-1.71.71", "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": 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": "Q7Z5L9-1.175.175", "start_pos": 175, "end_pos": 175, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Phosphoproteomic analysis of distinct tumor cell lines in response to nocodazole treatment.", "journal": "Proteomics", "date": "2009", "authors": "Nagano K, Shinkawa T, Mutoh H, Kondoh O, Morimoto S, Inomata N, Ashihara M, Ishii N, Aoki Y, Haramura M", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658", "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": "GILVPNGFSKLEEPPELNRQ", "down_seq": "PNPRRGHAVPPTLVPLMNGS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser175" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q7Z5L9-1.195.195", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.195.195", "start_pos": 195, "end_pos": 195, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies.", "journal": "Molecular immunology", "date": "2020-07", "authors": "Pandey Kirti, Mifsud Nicole A, Lim Kam Sian Terry C C, Ayala Rochelle, Ternette Nicola, Ramarathinam Sri H, Purcell Anthony W", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "IEDB", "id": "437472", "url": "https://www.iedb.org/epitope/437472" }, { "database": "IEDB", "id": "445176", "url": "https://www.iedb.org/epitope/445176" }, { "database": "IEDB", "id": "453936", "url": "https://www.iedb.org/epitope/453936" }, { "database": "IEDB", "id": "454766", "url": "https://www.iedb.org/epitope/454766" }, { "database": "IEDB", "id": "1348084", "url": "https://www.iedb.org/epitope/1348084" }, { "database": "IEDB", "id": "1348512", "url": "https://www.iedb.org/epitope/1348512" }, { "database": "IEDB", "id": "1356581", "url": "https://www.iedb.org/epitope/1356581" }, { "database": "IEDB", "id": "1366309", "url": "https://www.iedb.org/epitope/1366309" }, { "database": "IEDB", "id": "1374449", "url": "https://www.iedb.org/epitope/1374449" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "https://www.iedb.org/epitope/Q7Z5L9", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPNPRRGHAVPPTLVPLMNG", "down_seq": "ATPLPTALGLGGRAAASLAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q7Z5L9", "url": "https://www.iedb.org/epitope/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ], "site_lbl": "Ser195" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q7Z5L9-1.175.175", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q7Z5L9-1.212.212", "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": "Q7Z5L9-1.318.318", "start_pos": 318, "end_pos": 318, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] }, { "title": "In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies.", "journal": "Molecular immunology", "date": "2020-07", "authors": "Pandey Kirti, Mifsud Nicole A, Lim Kam Sian Terry C C, Ayala Rochelle, Ternette Nicola, Ramarathinam Sri H, Purcell Anthony W", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "IEDB", "id": "437472", "url": "https://www.iedb.org/epitope/437472" }, { "database": "IEDB", "id": "445176", "url": "https://www.iedb.org/epitope/445176" }, { "database": "IEDB", "id": "453936", "url": "https://www.iedb.org/epitope/453936" }, { "database": "IEDB", "id": "454766", "url": "https://www.iedb.org/epitope/454766" }, { "database": "IEDB", "id": "1348084", "url": "https://www.iedb.org/epitope/1348084" }, { "database": "IEDB", "id": "1348512", "url": "https://www.iedb.org/epitope/1348512" }, { "database": "IEDB", "id": "1356581", "url": "https://www.iedb.org/epitope/1356581" }, { "database": "IEDB", "id": "1366309", "url": "https://www.iedb.org/epitope/1366309" }, { "database": "IEDB", "id": "1374449", "url": "https://www.iedb.org/epitope/1374449" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "https://www.iedb.org/epitope/Q7Z5L9", "database": "IEDB", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WVNRPKTVRDTLLALHQHGH", "down_seq": "GPFESKFKKEPALTAGRLLG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" }, { "database": "IEDB", "id": "Q7Z5L9", "url": "https://www.iedb.org/epitope/Q7Z5L9" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ], "site_lbl": "Ser318" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q7Z5L9-1.302.302", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7Z5L9-1.323.323", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.323.323", "start_pos": 323, "end_pos": 323, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KTVRDTLLALHQHGHSGPFE", "down_seq": "KFKKEPALTAGRLLGFEANG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser323" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q7Z5L9-1.318.318", "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": "Q7Z5L9-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "Identification of a phosphorylation-dependent nuclear localization motif in interferon regulatory factor 2 binding protein 2.", "journal": "PloS one", "date": "2011", "authors": "Teng AC, Al-Montashiri NA, Cheng BL, Lou P, Ozmizrak P, Chen HH, Stewart AF", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "21887377", "url": "https://glygen.org/publication/PubMed/21887377" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008", "authors": "McNulty DE, Annan RS", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Immobilized metal affinity chromatography revisited: pH/acid control toward high selectivity in phosphoproteomics.", "journal": "Journal of proteome research", "date": "2008", "authors": "Tsai CF, Wang YT, Chen YR, Lai CY, Lin PY, Pan KT, Chen JY, Khoo KH, Chen YJ", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] }, { "title": "Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer.", "journal": "Analytical chemistry", "date": "2010", "authors": "Raijmakers R, Kraiczek K, de Jong AP, Mohammed S, Heck AJ", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] }, { "title": "NLS-tagging: an alternative strategy to tag nuclear proteins.", "journal": "Nucleic acids research", "date": "2014", "authors": "Giraud G, Stadhouders R, Conidi A, Dekkers DH, Huylebroeck D, Demmers JA, Soler E, Grosveld FG", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "25260593", "url": "https://glygen.org/publication/PubMed/25260593" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21887377", "url": "https://glygen.org/publication/PubMed/21887377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25260593", "url": "https://glygen.org/publication/PubMed/25260593", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EANGANGSKAVARTARKRKP", "down_seq": "PEPEGEVGPPKINGEAQPWL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "21887377", "url": "https://glygen.org/publication/PubMed/21887377" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" }, { "database": "PubMed", "id": "25260593", "url": "https://glygen.org/publication/PubMed/25260593" } ], "site_lbl": "Ser360" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "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": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.406.406", "start_pos": 406, "end_pos": 406, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "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": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "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": "GLKIPMTPTSSFVSPPPPTA", "down_seq": "PHSNRTTPPEAAQNGQSPMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser406" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5L9-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5L9-1.404.404", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5L9-1.409.409", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q7Z5L9-1.412.412", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z5L9-1.413.413", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q7Z5L9-1.423.423", "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": "Q7Z5L9-1.412.412", "start_pos": 412, "end_pos": 412, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TPTSSFVSPPPPTASPHSNR", "down_seq": "TPPEAAQNGQSPMAALILVA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Thr412" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q7Z5L9-1.392.392", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q7Z5L9-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q7Z5L9-1.404.404", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q7Z5L9-1.406.406", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5L9-1.409.409", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5L9-1.413.413", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7Z5L9-1.423.423", "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": "Q7Z5L9-1.413.413", "start_pos": 413, "end_pos": 413, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PTSSFVSPPPPTASPHSNRT", "down_seq": "PPEAAQNGQSPMAALILVAD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Thr413" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q7Z5L9-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q7Z5L9-1.396.396", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q7Z5L9-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q7Z5L9-1.404.404", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5L9-1.406.406", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5L9-1.409.409", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5L9-1.412.412", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z5L9-1.423.423", "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": "Q7Z5L9-1.423.423", "start_pos": 423, "end_pos": 423, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "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": "PTASPHSNRTTPPEAAQNGQ", "down_seq": "PMAALILVADNAGGSHASKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser423" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q7Z5L9-1.404.404", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q7Z5L9-1.406.406", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q7Z5L9-1.409.409", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q7Z5L9-1.412.412", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q7Z5L9-1.413.413", "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": "Q7Z5L9-1.457.457", "start_pos": 457, "end_pos": 457, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSHASKDANQVHSTTRRNSN", "down_seq": "PPSPSSMNQRRLGPREVGGQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser457" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q7Z5L9-1.448.448", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5L9-1.455.455", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5L9-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5L9-1.458.458", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5L9-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q7Z5L9-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q7Z5L9-1.463.463", "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": "Q7Z5L9-1.460.460", "start_pos": 460, "end_pos": 460, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASKDANQVHSTTRRNSNSPP", "down_seq": "PSSMNQRRLGPREVGGQGAG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Ser460" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q7Z5L9-1.448.448", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q7Z5L9-1.455.455", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5L9-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5L9-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5L9-1.458.458", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z5L9-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q7Z5L9-1.463.463", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.462.462", "start_pos": 462, "end_pos": 462, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "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": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "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": "KDANQVHSTTRRNSNSPPSP", "down_seq": "SMNQRRLGPREVGGQGAGNT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser462" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q7Z5L9-1.448.448", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5L9-1.455.455", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q7Z5L9-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q7Z5L9-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q7Z5L9-1.458.458", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z5L9-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q7Z5L9-1.463.463", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z5L9-1.463.463", "start_pos": 463, "end_pos": 463, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "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": "DANQVHSTTRRNSNSPPSPS", "down_seq": "MNQRRLGPREVGGQGAGNTG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser463" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q7Z5L9-1.448.448", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q7Z5L9-1.455.455", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z5L9-1.456.456", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q7Z5L9-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q7Z5L9-1.458.458", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q7Z5L9-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q7Z5L9-1.462.462", "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": "Q7Z5L9-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "Q7Z5L9-1", "length": 587, "uniprot_id": "I2BP2_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 2", "refseq_ac": "NP_001070865", "refseq_name": "interferon regulatory factor 2-binding protein 2 isoform B", "gene_name": "IRF2BP2", "gene_names_uniprotkb": "IRF2BP2", "gene_names_refseq": "CVID14; IRF2BP2; LRIR2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" } ], "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": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FVIETARQLKRAHGCFPEGR", "down_seq": "PPGAAASAAAKPPPLSAKDI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q7Z5L9", "url": "https://www.uniprot.org/uniprotkb/Q7Z5L9" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q7Z5L9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7Z5L9" } ], "site_lbl": "Ser71" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "409", "end_pos": "409" } ] }, { "type": "snv", "site_list": [ { "start_pos": "141", "end_pos": "141" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q7Z5L9-1.78.78", "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": "Q8IU81-1.457.457", "start_pos": 457, "end_pos": 457, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q8IU81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1967027844", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1967027844", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1967027844", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1967027844#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PKDPGGGGGPVRAGGASPAA", "down_seq": "STAQPPTQHRLVARNGEAEV", "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": "Ser457", "evidence": [ { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "Q8IU81", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ] } ], "snv": [ { "evidence": [ { "id": "Q8IU81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81" }, { "id": "rs1967027844", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1967027844" }, { "id": "rs1967027844", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1967027844#frequency_tab" } ], "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": "19", "chr_pos": "45884405", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S457", "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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "site_lbl": "Ser457" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IU81-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IU81-1.458.458", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IU81-1.459.459", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IU81-1.464.464", "categories": [ "glycosylation_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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IU81-1.458.458", "start_pos": 458, "end_pos": 458, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" }, { "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": "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Cell-type-specific labeling and profiling of glycans in living mice.", "journal": "Nature chemical biology", "date": "2022-06", "authors": "Fan Xinqi, Song Qitao, Sun De-En, Hao Yi, Wang Jingyang, Wang Chunting, Chen Xing", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511" } ] }, { "title": "OGA mutant aberrantly hydrolyzes O-GlcNAc modification from PDLIM7 to modulate p53 and cytoskeleton in promoting cancer cell malignancy.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-06-11", "authors": "Hu Chia-Wei, Wang Ao, Fan Dacheng, Worth Matthew, Chen Zhengwei, Huang Junfeng, Xie Jinshan, Macdonald John, Li Lingjun, Jiang Jiaoyang", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "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": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs994846468", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs994846468", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs994846468", "url": "http://gnomad.broadinstitute.org/awesome?query=rs994846468", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KDPGGGGGPVRAGGASPAAS", "down_seq": "TAQPPTQHRLVARNGEAEVS", "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": "Ser458", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q8IU81", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "Q8IU81", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8IU81" }, { "id": "35513511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35513511" }, { "id": "38838015", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38838015" } ] }, { "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": "Ser458", "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": "Q8IU81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81" }, { "id": "rs994846468", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs994846468" }, { "id": "rs994846468", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs994846468" } ], "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": "19", "chr_pos": "45884402", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S458", "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": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8IU81-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IU81-1.457.457", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IU81-1.459.459", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IU81-1.464.464", "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": 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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IU81-1.459.459", "start_pos": 459, "end_pos": 459, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" }, { "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": "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "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": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs779357576", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779357576", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779357576", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779357576", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779357576", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779357576#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779357576", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779357576", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DPGGGGGPVRAGGASPAASS", "down_seq": "AQPPTQHRLVARNGEAEVSP", "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": "Thr459", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q8IU81", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "Q8IU81", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ] } ], "snv": [ { "evidence": [ { "id": "rs779357576", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779357576" }, { "id": "rs779357576", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779357576" }, { "id": "rs779357576", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779357576#frequency_tab" }, { "id": "rs779357576", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779357576" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "19", "chr_pos": "45884399", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T459", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8IU81-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IU81-1.457.457", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IU81-1.458.458", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IU81-1.464.464", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IU81-1.464.464", "start_pos": 464, "end_pos": 464, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" }, { "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": "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "database": "O-GlcNAc Atlas", "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "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": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "https://oglcnac.org/atlas/detail/Q8IU81", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GGPVRAGGASPAASSTAQPP", "down_seq": "QHRLVARNGEAEVSPTAGAE", "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": "Thr464", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q8IU81", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IU81" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "Q8IU81", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8IU81" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8IU81-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8IU81-1.457.457", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IU81-1.458.458", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IU81-1.459.459", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IU81-1.480.480", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IU81-1.480.480", "start_pos": 480, "end_pos": 480, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "AQPPTQHRLVARNGEAEVSP", "down_seq": "AGAEAVSGGGSGTGATPGAP", "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": "Thr480", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8IU81-1.464.464", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IU81-1.491.491", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IU81-1.493.493", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IU81-1.496.496", "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": 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": "Q8IU81-1.496.496", "start_pos": 496, "end_pos": 496, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "EVSPTAGAEAVSGGGSGTGA", "down_seq": "PGAPLCCTLCRERLEDTHFV", "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": "Thr496", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8IU81-1.480.480", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IU81-1.491.491", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IU81-1.493.493", "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": 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": "Q8IU81-1.214.214", "start_pos": 214, "end_pos": 214, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1386931859", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386931859", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1386931859", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386931859", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SDFEKEKQQRNADCLAELNE", "down_seq": "MRGRAEEWHGRPKAVREQLL", "snv": [ { "evidence": [ { "id": "rs1386931859", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386931859" }, { "id": "rs1386931859", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386931859" } ], "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": "19", "chr_pos": "45885135", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A214", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": "Q8IU81-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IU81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RPKAVREQLLALSACAPFNV", "down_seq": "FKKDHGLVGRVFAFDATARP", "snv": [ { "evidence": [ { "id": "Q8IU81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81" } ], "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 (NVR->NVC).", "chr_id": "19", "chr_pos": "45885042", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R245", "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": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q8IU81-1.260.260", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8IU81-1.260.260", "start_pos": 260, "end_pos": 260, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IU81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "APFNVRFKKDHGLVGRVFAF", "down_seq": "ATARPPGYEFELKLFTEYPC", "snv": [ { "evidence": [ { "id": "Q8IU81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81" } ], "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 (DAT->NAT).", "chr_id": "19", "chr_pos": "45884997", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D260", "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": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IU81-1.245.245", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8IU81-1.375.375", "start_pos": 375, "end_pos": 375, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IU81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PEPAPAALCGPPPRAPSRNL", "down_seq": "PTPRRRKASPEPEGEAAGKM", "snv": [ { "evidence": [ { "id": "Q8IU81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81" } ], "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": "19", "chr_pos": "45884651", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A375", "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": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IU81-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IU81-1.384.384", "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": "Q8IU81-1.424.424", "start_pos": 424, "end_pos": 424, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IU81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HWVAPGGPYSAETPGVPSPI", "down_seq": "ALKNVAEALGHSPKDPGGGG", "snv": [ { "evidence": [ { "id": "Q8IU81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "45884504", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A424", "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: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": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8IU81-1.421.421", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IU81-1.430.430", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IU81-1.436.436", "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": "Q8IU81-1.430.430", "start_pos": 430, "end_pos": 430, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IU81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GPYSAETPGVPSPIAALKNV", "down_seq": "EALGHSPKDPGGGGGPVRAG", "snv": [ { "evidence": [ { "id": "Q8IU81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "45884486", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A430", "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": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IU81-1.421.421", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IU81-1.424.424", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IU81-1.436.436", "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": "Q8IU81-1.491.491", "start_pos": 491, "end_pos": 491, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8IU81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "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": "RNGEAEVSPTAGAEAVSGGG", "down_seq": "GTGATPGAPLCCTLCRERLE", "snv": [ { "evidence": [ { "id": "Q8IU81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81" } ], "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 (SGT->NGT).", "chr_id": "19", "chr_pos": "45884303", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S491", "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: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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser491" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8IU81-1.480.480", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IU81-1.493.493", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IU81-1.496.496", "categories": [ "glycosylation_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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8IU81-1.537.537", "start_pos": 537, "end_pos": 537, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IU81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QCPSVPGHKFCFPCSREFIK", "down_seq": "QGPAGEVYCPSGDKCPLVGS", "snv": [ { "evidence": [ { "id": "Q8IU81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "45884165", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A537", "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: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": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q8IU81-1.550.550", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8IU81-1.550.550", "start_pos": 550, "end_pos": 550, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1967023381", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1967023381", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1967023381", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1967023381#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "CSREFIKAQGPAGEVYCPSG", "down_seq": "KCPLVGSSVPWAFMQGEIAT", "snv": [ { "evidence": [ { "id": "rs1967023381", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1967023381" }, { "id": "rs1967023381", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1967023381#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DKC->NKC).", "chr_id": "19", "chr_pos": "45884127", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D550", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IU81-1.537.537", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IU81-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IU81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "MASV", "down_seq": "ASRRQWCYLCDLPKMPWAMV", "snv": [ { "evidence": [ { "id": "Q8IU81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IU81" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "45885762", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q5", "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": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": "Q8IU81-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis.", "journal": "Journal of proteome research", "date": "2008", "authors": "Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" } ] } ], "crossref": [ { "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GVSGQDRYDRATSSGRLPLP", "down_seq": "PALEYTLGSRLANGLGREEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "site_lbl": "Ser125" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IU81-1.186.186", "start_pos": 186, "end_pos": 186, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "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": "LLAAAVSGLGSRGLTLAPGL", "down_seq": "PARPLFGSDFEKEKQQRNAD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser186" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IU81-1.371.371", "start_pos": 371, "end_pos": 371, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PQQYPEPAPAALCGPPPRAP", "down_seq": "RNLAPTPRRRKASPEPEGEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "site_lbl": "Ser371" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8IU81-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IU81-1.384.384", "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": "Q8IU81-1.384.384", "start_pos": 384, "end_pos": 384, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008", "authors": "McNulty DE, Annan RS", "evidence": [ { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "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": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GPPPRAPSRNLAPTPRRRKA", "down_seq": "PEPEGEAAGKMTTEEQQQRH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser384" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IU81-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IU81-1.375.375", "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": "Q8IU81-1.421.421", "start_pos": 421, "end_pos": 421, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQRHWVAPGGPYSAETPGVP", "down_seq": "PIAALKNVAEALGHSPKDPG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "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": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser421" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8IU81-1.424.424", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IU81-1.430.430", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IU81-1.436.436", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IU81-1.436.436", "start_pos": 436, "end_pos": 436, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "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": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPGVPSPIAALKNVAEALGH", "down_seq": "PKDPGGGGGPVRAGGASPAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser436" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IU81-1.421.421", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8IU81-1.424.424", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IU81-1.430.430", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IU81-1.453.453", "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": "Q8IU81-1.453.453", "start_pos": 453, "end_pos": 453, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis.", "journal": "Journal of proteome research", "date": "2008", "authors": "Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "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": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336", "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": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "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": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGHSPKDPGGGGGPVRAGGA", "down_seq": "PAASSTAQPPTQHRLVARNG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" }, { "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": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "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": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Ser453" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IU81-1.436.436", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IU81-1.457.457", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IU81-1.458.458", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IU81-1.459.459", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IU81-1.464.464", "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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IU81-1.493.493", "start_pos": 493, "end_pos": 493, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "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": "GEAEVSPTAGAEAVSGGGSG", "down_seq": "GATPGAPLCCTLCRERLEDT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr493" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IU81-1.480.480", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IU81-1.491.491", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IU81-1.496.496", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IU81-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "Q8IU81-1", "length": 584, "uniprot_id": "I2BP1_HUMAN", "protein_name": "Interferon regulatory factor 2-binding protein 1", "refseq_ac": "NP_056464", "refseq_name": "interferon regulatory factor 2-binding protein 1", "gene_name": "IRF2BP1", "gene_names_uniprotkb": "IRF2BP1", "gene_names_refseq": "IRF2BP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" } ], "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELLIDAARQLKRSHVLPEGR", "down_seq": "PGPPALKHPATKDLAAAAAQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IU81", "url": "https://www.uniprot.org/uniprotkb/Q8IU81" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q8IU81", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IU81" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser66" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "496", "end_pos": "496" } ] }, { "type": "snv", "site_list": [ { "start_pos": "214", "end_pos": "214" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "537", "end_pos": "537" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.188.188", "start_pos": 188, "end_pos": 188, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q9BW71", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "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": "Q9BW71", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "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": "Q9BW71", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] } ], "crossref": [ { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BW71", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1019037181", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1019037181", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1019037181", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1019037181#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1019037181", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1019037181", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KGKTRKKPVVKKQAPGKASV", "down_seq": "RKQAREESEESEAEPVQRTA", "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": "Ser188", "evidence": [ { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "Q9BW71", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BW71" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" } ] } ], "snv": [ { "evidence": [ { "id": "rs1019037181", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1019037181" }, { "id": "rs1019037181", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1019037181#frequency_tab" }, { "id": "rs1019037181", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1019037181" } ], "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": "16", "chr_pos": "29994581", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S188", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BW71-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BW71-1.199.199", "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": 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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BW71", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BW71", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EKGYKGKTRKKPVVKKQAPG", "down_seq": "ASVSRKQAREESEESEAEPV", "snv": [ { "evidence": [ { "id": "Q9BW71", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BW71" } ], "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 (KAS->NAS).", "chr_id": "16", "chr_pos": "29994593", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K184", "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": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9BW71-1.167.167", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.188.188", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9BW71-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9BW71-1.199.199", "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": "Q9BW71-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BW71", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BW71", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs371999310", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371999310", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371999310", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371999310", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371999310", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371999310#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371999310", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371999310", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EESEAEPVQRTAKKVEGNKG", "down_seq": "KSLKESEQESEEEILAQKKE", "snv": [ { "evidence": [ { "id": "Q9BW71", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BW71" }, { "id": "rs371999310", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371999310" }, { "id": "rs371999310", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371999310" }, { "id": "rs371999310", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371999310#frequency_tab" }, { "id": "rs371999310", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371999310" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TKS->NKS).", "chr_id": "16", "chr_pos": "29994495", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T217", "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": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BW71-1.199.199", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BW71-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BW71-1.223.223", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BW71-1.227.227", "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": "Q9BW71-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BW71", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BW71", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ASSGDDSGRDREPPVQRKSE", "down_seq": "RTQLKGGKRLSGSSEDEEDS", "snv": [ { "evidence": [ { "id": "Q9BW71", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BW71" } ], "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 (DRT->NRT).", "chr_id": "16", "chr_pos": "29994190", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D319", "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": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9BW71-1.300.300", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9BW71-1.301.301", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9BW71-1.305.305", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BW71-1.330.330", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9BW71-1.332.332", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BW71-1.333.333", "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": "Q9BW71-1.373.373", "start_pos": 373, "end_pos": 373, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BW71", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BW71", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ARLGSTSGEESDLEREVSDS", "down_seq": "AGGGPQGERKNRSSKKSSRK", "snv": [ { "evidence": [ { "id": "Q9BW71", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BW71" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "29994028", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E373", "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": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9BW71-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9BW71-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9BW71-1.359.359", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9BW71-1.363.363", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BW71-1.370.370", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9BW71-1.372.372", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9BW71-1.388.388", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q9BW71-1.388.388", "start_pos": 388, "end_pos": 388, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2070025076", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2070025076", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2070025076", "url": "https://www.ensembl.org/id/rs2070025076", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EVSDSEAGGGPQGERKNRSS", "down_seq": "KSSRKGRTRSSSSSSDGSPE", "snv": [ { "evidence": [ { "id": "rs2070025076", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2070025076" }, { "id": "rs2070025076", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2070025076" } ], "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": "16", "chr_pos": "29993981", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K388", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BW71-1.370.370", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9BW71-1.372.372", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9BW71-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BW71-1.404.404", "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": "Q9BW71-1.404.404", "start_pos": 404, "end_pos": 404, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764484615", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764484615", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764484615", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764484615", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764484615", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764484615#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764484615", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764484615", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NRSSKKSSRKGRTRSSSSSS", "down_seq": "GSPEAKGGKAGSGRRGEDHP", "snv": [ { "evidence": [ { "id": "rs764484615", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764484615" }, { "id": "rs764484615", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764484615" }, { "id": "rs764484615", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764484615#frequency_tab" }, { "id": "rs764484615", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764484615" } ], "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": "16", "chr_pos": "29993935", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D404", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9BW71-1.388.388", "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": "Q9BW71-1.500.500", "start_pos": 500, "end_pos": 500, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs961018748", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs961018748", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs961018748", "url": "http://gnomad.broadinstitute.org/awesome?query=rs961018748", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKEQREEAAEVASLDVANII", "down_seq": "GSGRPRRRTAWNPLGEAAPP", "snv": [ { "evidence": [ { "id": "rs961018748", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs961018748" }, { "id": "rs961018748", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs961018748" } ], "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": "16", "chr_pos": "29993467", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S500", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "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": "Q9BW71-1.546.546", "start_pos": 546, "end_pos": 546, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BW71", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BW71", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RTLDSDEERPRPAPPDWSHM", "down_seq": "GIISSDGESN", "snv": [ { "evidence": [ { "id": "Q9BW71", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BW71" } ], "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": "16", "chr_pos": "29993242", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R546", "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": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9BW71-1.530.530", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.550.550", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BW71-1.551.551", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BW71-1.555.555", "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": "Q9BW71-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KRPPTPCSDPERKRFRFNSE", "down_seq": "ESGSEASSPDYFGPPAKNGV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser100" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9BW71-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9BW71-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BW71-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BW71-1.102.102", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.104.104", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9BW71-1.107.107", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BW71-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BW71-1.111.111", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPTPCSDPERKRFRFNSESE", "down_seq": "GSEASSPDYFGPPAKNGVAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser102" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BW71-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9BW71-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BW71-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BW71-1.104.104", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BW71-1.107.107", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BW71-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BW71-1.111.111", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPCSDPERKRFRFNSESESG", "down_seq": "EASSPDYFGPPAKNGVAAEV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser104" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9BW71-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9BW71-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BW71-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BW71-1.102.102", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BW71-1.107.107", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9BW71-1.111.111", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SDPERKRFRFNSESESGSEA", "down_seq": "SPDYFGPPAKNGVAAEVSPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser107" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9BW71-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9BW71-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9BW71-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BW71-1.102.102", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BW71-1.104.104", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BW71-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.111.111", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BW71-1.125.125", "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": "Q9BW71-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "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": "DPERKRFRFNSESESGSEAS", "down_seq": "PDYFGPPAKNGVAAEVSPAK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser108" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9BW71-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9BW71-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BW71-1.102.102", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.104.104", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9BW71-1.107.107", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BW71-1.111.111", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BW71-1.125.125", "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": "Q9BW71-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RKRFRFNSESESGSEASSPD", "down_seq": "FGPPAKNGVAAEVSPAKEEN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Tyr111" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9BW71-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9BW71-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9BW71-1.102.102", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9BW71-1.104.104", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.107.107", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BW71-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BW71-1.125.125", "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": "Q9BW71-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EASSPDYFGPPAKNGVAAEV", "down_seq": "PAKEENPRRASKAVEESSDE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Ser125" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BW71-1.107.107", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9BW71-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9BW71-1.111.111", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BW71-1.136.136", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BW71-1.142.142", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BW71-1.143.143", "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": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AKNGVAAEVSPAKEENPRRA", "down_seq": "KAVEESSDEERQRDLPAQRG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ], "site_lbl": "Ser136" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9BW71-1.125.125", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BW71-1.142.142", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9BW71-1.143.143", "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": "Q9BW71-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "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": "AEVSPAKEENPRRASKAVEE", "down_seq": "SDEERQRDLPAQRGEESSEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser142" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9BW71-1.125.125", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BW71-1.136.136", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BW71-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BW71-1.159.159", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BW71-1.160.160", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "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": "EVSPAKEENPRRASKAVEES", "down_seq": "DEERQRDLPAQRGEESSEEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser143" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BW71-1.125.125", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9BW71-1.136.136", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9BW71-1.142.142", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BW71-1.159.159", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BW71-1.160.160", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VEESSDEERQRDLPAQRGEE", "down_seq": "SEEEEKGYKGKTRKKPVVKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser159" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9BW71-1.142.142", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9BW71-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BW71-1.160.160", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BW71-1.167.167", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "title": "Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Tang LY, Deng N, Wang LS, Dai J, Wang ZL, Jiang XS, Li SJ, Li L, Sheng QH, Wu DQ, Li L, Zeng R", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17693683", "url": "https://glygen.org/publication/PubMed/17693683" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17693683", "url": "https://glygen.org/publication/PubMed/17693683", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EESSDEERQRDLPAQRGEES", "down_seq": "EEEEKGYKGKTRKKPVVKKQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "PubMed", "id": "17693683", "url": "https://glygen.org/publication/PubMed/17693683" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser160" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BW71-1.142.142", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9BW71-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9BW71-1.159.159", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9BW71-1.167.167", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Tang LY, Deng N, Wang LS, Dai J, Wang ZL, Jiang XS, Li SJ, Li L, Sheng QH, Wu DQ, Li L, Zeng R", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17693683", "url": "https://glygen.org/publication/PubMed/17693683" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17693683", "url": "https://glygen.org/publication/PubMed/17693683", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RQRDLPAQRGEESSEEEEKG", "down_seq": "KGKTRKKPVVKKQAPGKASV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17693683", "url": "https://glygen.org/publication/PubMed/17693683" } ], "site_lbl": "Tyr167" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9BW71-1.159.159", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9BW71-1.160.160", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BW71-1.184.184", "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": "Q9BW71-1.196.196", "start_pos": 196, "end_pos": 196, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Global phosphoproteome of HT-29 human colon adenocarcinoma cells.", "journal": "Journal of proteome research", "date": "2005", "authors": "Kim JE, Tannenbaum SR, White FM", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "16083285", "url": "https://glygen.org/publication/PubMed/16083285" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008", "authors": "McNulty DE, Annan RS", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16083285", "url": "https://glygen.org/publication/PubMed/16083285", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VVKKQAPGKASVSRKQAREE", "down_seq": "EESEAEPVQRTAKKVEGNKG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "16083285", "url": "https://glygen.org/publication/PubMed/16083285" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser196" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9BW71-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9BW71-1.188.188", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BW71-1.199.199", "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": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008", "authors": "McNulty DE, Annan RS", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KQAPGKASVSRKQAREESEE", "down_seq": "EAEPVQRTAKKVEGNKGTKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser199" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9BW71-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9BW71-1.188.188", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BW71-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BW71-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9BW71-1.219.219", "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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.219.219", "start_pos": 219, "end_pos": 219, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "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": "SEAEPVQRTAKKVEGNKGTK", "down_seq": "LKESEQESEEEILAQKKEQR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser219" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9BW71-1.199.199", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BW71-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.223.223", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BW71-1.227.227", "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": "Q9BW71-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "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": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "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": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PVQRTAKKVEGNKGTKSLKE", "down_seq": "EQESEEEILAQKKEQREEEV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Ser223" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9BW71-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.227.227", "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": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.227.227", "start_pos": 227, "end_pos": 227, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "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": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TAKKVEGNKGTKSLKESEQE", "down_seq": "EEEILAQKKEQREEEVEEEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "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": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Ser227" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9BW71-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9BW71-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.223.223", "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": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "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": "MQEFTRSFFRGRPDLSTLTH", "down_seq": "IVRRRYLAHSGRSHLEPEEK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "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": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser27" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.289.289", "start_pos": 289, "end_pos": 289, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SAREERSCKQKSQAKRLLGD", "down_seq": "DSEEEQKEAASSGDDSGRDR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser289" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9BW71-1.291.291", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BW71-1.300.300", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9BW71-1.301.301", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BW71-1.305.305", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.291.291", "start_pos": 291, "end_pos": 291, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "REERSCKQKSQAKRLLGDSD", "down_seq": "EEEQKEAASSGDDSGRDREP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser291" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9BW71-1.289.289", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BW71-1.300.300", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BW71-1.301.301", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BW71-1.305.305", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SQAKRLLGDSDSEEEQKEAA", "down_seq": "SGDDSGRDREPPVQRKSEDR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser300" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9BW71-1.289.289", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9BW71-1.291.291", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BW71-1.301.301", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BW71-1.305.305", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9BW71-1.319.319", "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": "Q9BW71-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QAKRLLGDSDSEEEQKEAAS", "down_seq": "GDDSGRDREPPVQRKSEDRT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser301" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9BW71-1.289.289", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9BW71-1.291.291", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9BW71-1.300.300", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.305.305", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BW71-1.319.319", "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": "Q9BW71-1.305.305", "start_pos": 305, "end_pos": 305, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLGDSDSEEEQKEAASSGDD", "down_seq": "GRDREPPVQRKSEDRTQLKG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser305" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9BW71-1.289.289", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9BW71-1.291.291", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BW71-1.300.300", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.301.301", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BW71-1.319.319", "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": "Q9BW71-1.330.330", "start_pos": 330, "end_pos": 330, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EPPVQRKSEDRTQLKGGKRL", "down_seq": "GSSEDEEDSGKGEPTAKGSR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser330" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9BW71-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BW71-1.332.332", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BW71-1.333.333", "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": "Q9BW71-1.332.332", "start_pos": 332, "end_pos": 332, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "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": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PVQRKSEDRTQLKGGKRLSG", "down_seq": "SEDEEDSGKGEPTAKGSRKM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "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": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser332" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9BW71-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BW71-1.330.330", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BW71-1.333.333", "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": "Q9BW71-1.333.333", "start_pos": 333, "end_pos": 333, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VQRKSEDRTQLKGGKRLSGS", "down_seq": "EDEEDSGKGEPTAKGSRKMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser333" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q9BW71-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BW71-1.330.330", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9BW71-1.332.332", "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": "Q9BW71-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EDSGKGEPTAKGSRKMARLG", "down_seq": "TSGEESDLEREVSDSEAGGG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser357" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q9BW71-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BW71-1.359.359", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BW71-1.363.363", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9BW71-1.370.370", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9BW71-1.372.372", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BW71-1.373.373", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.358.358", "start_pos": 358, "end_pos": 358, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "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" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DSGKGEPTAKGSRKMARLGS", "down_seq": "SGEESDLEREVSDSEAGGGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Thr358" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q9BW71-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BW71-1.359.359", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BW71-1.363.363", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9BW71-1.370.370", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BW71-1.372.372", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9BW71-1.373.373", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.359.359", "start_pos": 359, "end_pos": 359, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGKGEPTAKGSRKMARLGST", "down_seq": "GEESDLEREVSDSEAGGGPQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser359" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9BW71-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9BW71-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.363.363", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BW71-1.370.370", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9BW71-1.372.372", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BW71-1.373.373", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.363.363", "start_pos": 363, "end_pos": 363, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "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": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EPTAKGSRKMARLGSTSGEE", "down_seq": "DLEREVSDSEAGGGPQGERK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser363" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9BW71-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BW71-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.359.359", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9BW71-1.370.370", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BW71-1.372.372", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BW71-1.373.373", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.370.370", "start_pos": 370, "end_pos": 370, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "RKMARLGSTSGEESDLEREV", "down_seq": "DSEAGGGPQGERKNRSSKKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser370" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9BW71-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9BW71-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9BW71-1.359.359", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9BW71-1.363.363", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BW71-1.372.372", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BW71-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BW71-1.388.388", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.372.372", "start_pos": 372, "end_pos": 372, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MARLGSTSGEESDLEREVSD", "down_seq": "EAGGGPQGERKNRSSKKSSR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser372" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9BW71-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9BW71-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9BW71-1.359.359", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9BW71-1.363.363", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BW71-1.370.370", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BW71-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BW71-1.388.388", "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": "Q9BW71-1.471.471", "start_pos": 471, "end_pos": 471, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "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": "SHKERLSILRAELEALGMKG", "down_seq": "PSLGKCRALKEQREEAAEVA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr471" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.530.530", "start_pos": 530, "end_pos": 530, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "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": "AWNPLGEAAPPGELYRRTLD", "down_seq": "DEERPRPAPPDWSHMRGIIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "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": "Ser530" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q9BW71-1.546.546", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9BW71-1.550.550", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.550.550", "start_pos": 550, "end_pos": 550, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "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": "SDEERPRPAPPDWSHMRGII", "down_seq": "SDGESN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser550" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9BW71-1.530.530", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.546.546", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BW71-1.551.551", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BW71-1.555.555", "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": "Q9BW71-1.551.551", "start_pos": 551, "end_pos": 551, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "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": "DEERPRPAPPDWSHMRGIIS", "down_seq": "DGESN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser551" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9BW71-1.546.546", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9BW71-1.550.550", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.555.555", "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": "Q9BW71-1.555.555", "start_pos": 555, "end_pos": 555, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "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": "PRPAPPDWSHMRGIISSDGE", "down_seq": "", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser555" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q9BW71-1.546.546", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BW71-1.550.550", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BW71-1.551.551", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008", "authors": "McNulty DE, Annan RS", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Phosphoproteomic analysis of distinct tumor cell lines in response to nocodazole treatment.", "journal": "Proteomics", "date": "2009", "authors": "Nagano K, Shinkawa T, Mutoh H, Kondoh O, Morimoto S, Inomata N, Ashihara M, Ishii N, Aoki Y, Haramura M", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DEAASREDKLDLTKKGKRPP", "down_seq": "PCSDPERKRFRFNSESESGS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ], "site_lbl": "Thr84" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q9BW71-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BW71-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BW71-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BW71-1.102.102", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9BW71-1.104.104", "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": "Q9BW71-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Phosphoproteomic analysis of distinct tumor cell lines in response to nocodazole treatment.", "journal": "Proteomics", "date": "2009", "authors": "Nagano K, Shinkawa T, Mutoh H, Kondoh O, Morimoto S, Inomata N, Ashihara M, Ishii N, Aoki Y, Haramura M", "evidence": [ { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASREDKLDLTKKGKRPPTPC", "down_seq": "DPERKRFRFNSESESGSEAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ], "site_lbl": "Ser87" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q9BW71-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BW71-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9BW71-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9BW71-1.102.102", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BW71-1.104.104", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9BW71-1.107.107", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BW71-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "Q9BW71-1", "length": 556, "uniprot_id": "HIRP3_HUMAN", "protein_name": "HIRA-interacting protein 3", "refseq_ac": "NP_001184252", "refseq_name": "HIRA-interacting protein 3 isoform 2", "gene_name": "HIRIP3", "gene_names_uniprotkb": "HIRIP3", "gene_names_refseq": "HIRIP3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" } ], "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": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "iPTMnet", "id": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "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": "Q9BW71-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KGKRPPTPCSDPERKRFRFN", "down_seq": "ESESGSEASSPDYFGPPAKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BW71", "url": "https://www.uniprot.org/uniprotkb/Q9BW71" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q9BW71", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BW71" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser98" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "188", "end_pos": "188" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "551", "end_pos": "551" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q9BW71-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9BW71-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BW71-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BW71-1.102.102", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BW71-1.104.104", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BW71-1.107.107", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BW71-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9BW71-1.111.111", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9NRM6-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "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" } ] }, { "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": "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": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "7UWL", "url": "https://www.rcsb.org/structure/7UWL", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7UWJ", "url": "https://www.rcsb.org/structure/7UWJ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7UWL|D|103", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7UWL|C|103", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7UWJ|D|103", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7UWJ|C|103", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs1348276631", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348276631", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1348276631", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1348276631", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs965523386", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs965523386", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs965523386", "url": "https://www.ensembl.org/id/rs965523386", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ATKICVTGKSNFQSYSCVRC", "down_seq": "YTEAFQTQTRPSGGKWTFSY", "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": "CnYTEAFQTQTRPSGGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn103", "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": "CNYTEAFQTQTR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn103", "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" }, { "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": "CnYTEAFQTQTRPSGGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn103", "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": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7UWL&bu=0&command=select+.D:103;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn103", "evidence": [ { "id": "Q9NRM6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6#ptm_processing" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "7UWL", "database": "PDB", "url": "https://www.rcsb.org/structure/7UWL" }, { "id": "7UWJ", "database": "PDB", "url": "https://www.rcsb.org/structure/7UWJ" } ] } ], "snv": [ { "evidence": [ { "id": "rs1348276631", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348276631" }, { "id": "rs1348276631", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1348276631" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NYT->DYT).", "chr_id": "3", "chr_pos": "53852079", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N103", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs965523386", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs965523386" }, { "id": "rs965523386", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs965523386" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NYT->SYT).", "chr_id": "3", "chr_pos": "53852080", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N103", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9NRM6-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9NRM6-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9NRM6-1.118.118", "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", "icn3d_view.label", "icn3d_view.url" ] }, { "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", "icn3d_view.label", "icn3d_view.url" ] }, { "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", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q9NRM6-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7UWL", "url": "https://www.rcsb.org/structure/7UWL", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7UWJ", "url": "https://www.rcsb.org/structure/7UWJ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7UWL|D|156", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7UWL|C|156", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7UWJ|D|156", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7UWJ|C|156", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs375626986", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375626986", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs375626986", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375626986", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs375626986", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375626986", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IGAHNIPNANMNEDGPSMSV", "down_seq": "FTSPGCLDHIMKYKKKCVKA", "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=7UWL&bu=0&command=select+.D:156;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn156", "evidence": [ { "id": "Q9NRM6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6#ptm_processing" }, { "id": "7UWL", "database": "PDB", "url": "https://www.rcsb.org/structure/7UWL" }, { "id": "7UWJ", "database": "PDB", "url": "https://www.rcsb.org/structure/7UWJ" } ] } ], "snv": [ { "evidence": [ { "id": "rs375626986", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375626986" }, { "id": "rs375626986", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375626986" }, { "id": "rs375626986", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375626986" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NFT->DFT).", "chr_id": "3", "chr_pos": "53852982", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N156", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "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": 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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NRM6-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "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" } ] }, { "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": "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": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "Q9NRM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NRM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LDHIMKYKKKCVKAGSLWDP", "down_seq": "ITACKKNEETVEVNFTTTPL", "glycosylation": [ { "glytoucan_ac": "G25079LO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AGSLWDPnITACK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn183", "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": "G46503DX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AGSLWDPNITACK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn183", "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": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AGSLWDPnITACK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn183", "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": "AGSLWDPnITACK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn183", "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": "G83460ZZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AGSLWDPnITACK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn183", "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": "Asn183", "evidence": [ { "id": "Q9NRM6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6#ptm_processing" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "snv": [ { "evidence": [ { "id": "Q9NRM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NRM6" } ], "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 (NIT->YIT).", "chr_id": "3", "chr_pos": "53856861", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N183", "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": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q9NRM6-1.197.197", "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": 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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9NRM6-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "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" } ] }, { "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": "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": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "7UWJ", "url": "https://www.rcsb.org/structure/7UWJ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7UWJ|D|197", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7UWJ|C|197", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GSLWDPNITACKKNEETVEV", "down_seq": "FTTTPLGNRYMALIQHSTII", "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": "KNEETVEVnFTTTPLGNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn197", "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": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KNEETVEVnFTTTPLGNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn197", "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": "KNEETVEVnFTTTPLGNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn197", "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": "KNEETVEVnFTTTPLGNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn197", "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": "KNEETVEVNFTTTPLGNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn197", "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" }, { "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": "G83460ZZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KNEETVEVnFTTTPLGNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn197", "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": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7UWJ&bu=0&command=select+.D:197;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn197", "evidence": [ { "id": "Q9NRM6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6#ptm_processing" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "7UWJ", "database": "PDB", "url": "https://www.rcsb.org/structure/7UWJ" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q9NRM6-1.183.183", "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": 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", "icn3d_view.label", "icn3d_view.url" ] }, { "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", "icn3d_view.label", "icn3d_view.url" ] }, { "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", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q9NRM6-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1056088555", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1056088555", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1056088555", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1056088555#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RHKGTVVLCPQTGVPFPLDN", "down_seq": "KSKPGGWLPLLLLSLLVATW", "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": "Asn283", "evidence": [ { "id": "Q9NRM6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1056088555", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1056088555" }, { "id": "rs1056088555", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1056088555#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKS->YKS).", "chr_id": "3", "chr_pos": "53858818", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N283", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9NRM6-1.265.265", "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": "Q9NRM6-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7UWL", "url": "https://www.rcsb.org/structure/7UWL", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7UWL|D|67", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7UWL|C|67", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs1699066584", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699066584", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1699066584", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1699066584#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1699066584", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1699066584", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs142019016", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142019016", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142019016", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142019016#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs142019016", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142019016", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DLRVEPVTTSVATGDYSILM", "down_seq": "VSWVLRADASIRLLKATKIC", "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=7UWL&bu=0&command=select+.D:67;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn67", "evidence": [ { "id": "Q9NRM6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6#ptm_processing" }, { "id": "7UWL", "database": "PDB", "url": "https://www.rcsb.org/structure/7UWL" } ] } ], "snv": [ { "evidence": [ { "id": "rs1699066584", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699066584" }, { "id": "rs1699066584", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1699066584#frequency_tab" }, { "id": "rs1699066584", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1699066584" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->IVS).", "chr_id": "3", "chr_pos": "53849769", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N67", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs142019016", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142019016" }, { "id": "rs142019016", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142019016#frequency_tab" }, { "id": "rs142019016", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142019016" } ], "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": "3", "chr_pos": "53849770", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N67", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1699066584", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699066584" }, { "id": "rs1699066584", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1699066584#frequency_tab" }, { "id": "rs1699066584", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1699066584" } ], "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": "3", "chr_pos": "53849769", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N67", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9NRM6-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9NRM6-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9NRM6-1.77.77", "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": 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": 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": "Q9NRM6-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1161655371", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1161655371", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1161655371", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1161655371", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1699170781", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699170781", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1699170781", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1699170781#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KICVTGKSNFQSYSCVRCNY", "down_seq": "EAFQTQTRPSGGKWTFSYIG", "snv": [ { "evidence": [ { "id": "rs1161655371", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1161655371" }, { "id": "rs1161655371", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1161655371" } ], "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 (NYT->NYA).", "chr_id": "3", "chr_pos": "53852085", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T105", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1699170781", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699170781" }, { "id": "rs1699170781", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1699170781#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NYT->NYK).", "chr_id": "3", "chr_pos": "53852086", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T105", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1161655371", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1161655371" }, { "id": "rs1161655371", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1161655371" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NYT->NYP).", "chr_id": "3", "chr_pos": "53852085", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T105", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9NRM6-1.103.103", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9NRM6-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9NRM6-1.118.118", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q9NRM6-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1699171534", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699171534", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1699171534", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1699171534#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1699171534", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1699171534", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GKSNFQSYSCVRCNYTEAFQ", "down_seq": "QTRPSGGKWTFSYIGFPVEL", "snv": [ { "evidence": [ { "id": "rs1699171534", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699171534" }, { "id": "rs1699171534", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1699171534#frequency_tab" }, { "id": "rs1699171534", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1699171534" } ], "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": "3", "chr_pos": "53852101", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T110", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9NRM6-1.103.103", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9NRM6-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9NRM6-1.118.118", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NRM6-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760618607", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760618607", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760618607", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760618607", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760618607", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760618607#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760618607", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760618607", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SCVRCNYTEAFQTQTRPSGG", "down_seq": "WTFSYIGFPVELNTVYFIGA", "snv": [ { "evidence": [ { "id": "rs760618607", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760618607" }, { "id": "rs760618607", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760618607" }, { "id": "rs760618607", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760618607#frequency_tab" }, { "id": "rs760618607", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760618607" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KWT->NWT).", "chr_id": "3", "chr_pos": "53852126", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K118", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9NRM6-1.103.103", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9NRM6-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9NRM6-1.110.110", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NRM6-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9NRM6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NRM6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QHSTIIGFSQVFEPHQKKQT", "down_seq": "ASVVIPVTGDSEGATVQLTP", "snv": [ { "evidence": [ { "id": "Q9NRM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NRM6" } ], "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": "3", "chr_pos": "53857637", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R232", "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" ] }, { "evidence": [ { "id": "Q9NRM6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9NRM6" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "53857638", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R232", "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: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": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "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": "Q9NRM6-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1699447201", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699447201", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1699447201", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1699447201", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GATVQLTPYFPTCGSDCIRH", "down_seq": "GTVVLCPQTGVPFPLDNNKS", "snv": [ { "evidence": [ { "id": "rs1699447201", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699447201" }, { "id": "rs1699447201", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1699447201" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KGT->NGT).", "chr_id": "3", "chr_pos": "53858766", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K265", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q9NRM6-1.283.283", "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": "Q9NRM6-1.405.405", "start_pos": 405, "end_pos": 405, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs745502642", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745502642", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745502642", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745502642", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745502642", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745502642#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs745502642", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745502642", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QKKAADKVVFLLSNDVNSVC", "down_seq": "GTCGKSEGSPSENSQDLFPL", "snv": [ { "evidence": [ { "id": "rs745502642", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745502642" }, { "id": "rs745502642", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745502642" }, { "id": "rs745502642", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745502642#frequency_tab" }, { "id": "rs745502642", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745502642" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DGT->NGT).", "chr_id": "3", "chr_pos": "53865012", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D405", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "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": "Q9NRM6-1.497.497", "start_pos": 497, "end_pos": 497, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs368854367", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368854367", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs368854367", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368854367", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs368854367", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368854367#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs368854367", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368854367", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AELLHVKQQVSAGKRSQACH", "down_seq": "GCCSL", "snv": [ { "evidence": [ { "id": "rs368854367", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368854367" }, { "id": "rs368854367", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368854367" }, { "id": "rs368854367", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368854367#frequency_tab" }, { "id": "rs368854367", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368854367" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DGC->NGC).", "chr_id": "3", "chr_pos": "53865288", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D497", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "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": "Q9NRM6-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756596770", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756596770", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756596770", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756596770", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756596770", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756596770#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs756596770", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756596770", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RVEPVTTSVATGDYSILMNV", "down_seq": "WVLRADASIRLLKATKICVT", "snv": [ { "evidence": [ { "id": "rs756596770", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756596770" }, { "id": "rs756596770", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756596770" }, { "id": "rs756596770", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756596770#frequency_tab" }, { "id": "rs756596770", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756596770" } ], "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 (NVS->NVN).", "chr_id": "3", "chr_pos": "53849775", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S69", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9NRM6-1.67.67", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9NRM6-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9NRM6-1.77.77", "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": "Q9NRM6-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1699068759", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699068759", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1699068759", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1699068759", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TSVATGDYSILMNVSWVLRA", "down_seq": "ASIRLLKATKICVTGKSNFQ", "snv": [ { "evidence": [ { "id": "rs1699068759", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1699068759" }, { "id": "rs1699068759", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1699068759" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DAS->NAS).", "chr_id": "3", "chr_pos": "53849792", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D75", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9NRM6-1.67.67", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9NRM6-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9NRM6-1.77.77", "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": "Q9NRM6-1.77.77", "start_pos": 77, "end_pos": 77, "uniprot_canonical_ac": "Q9NRM6-1", "length": 502, "uniprot_id": "I17RB_HUMAN", "protein_name": "Interleukin-17 receptor B", "refseq_ac": "NP_061195", "refseq_name": "interleukin-17 receptor B precursor", "gene_name": "IL17RB", "gene_names_uniprotkb": "IL17RB; CRL4; EVI27; IL17BR; PRO19612", "gene_names_refseq": "CRL4; EVI27; IL17BR; IL17RB; IL17RH1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NRM6", "url": "https://www.uniprot.org/uniprotkb/Q9NRM6" } ], "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": "Q9NRM6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NRM6" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "Q9NRM6", "url": "https://www.iedb.org/epitope/Q9NRM6", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q9NRM6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NRM6", "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": "VATGDYSILMNVSWVLRADA", "down_seq": "IRLLKATKICVTGKSNFQSY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q9NRM6", "url": "https://www.iedb.org/epitope/Q9NRM6" }, { "database": "iPTMnet", "id": "Q9NRM6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NRM6" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Ser77" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "67", "end_pos": "67" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9NRM6-1.67.67", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9NRM6-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9NRM6-1.75.75", "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": "Q9Y5N5-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "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": "rs1989429002", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1989429002", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1989429002", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1989429002", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LLPRLTEKVDLLVFNPPYVV", "down_seq": "PPQEVGSHGIEAAWAGGRNG", "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": "Thr128", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1989429002", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1989429002" }, { "id": "rs1989429002", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1989429002" } ], "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": "21", "chr_pos": "28879884", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T128", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9Y5N5-1.108.108", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9Y5N5-1.122.122", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9Y5N5-1.122.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9Y5N5-1.125.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9Y5N5-1.132.132", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9Y5N5-1.139.139", "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": 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": "Q9Y5N5-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "KMT9 monomethylates histone H4 lysine 12 and controls proliferation of prostate cancer cells.", "journal": "Nature structural & molecular biology", "date": "2019", "authors": "Metzger E, Wang S, Urban S, Willmann D, Schmidt A, Offermann A, Allen A, Sum M, Obier N, Cottard F, Ulferts S, Preca BT, Hermann B, Maurer J, Greschik H, Hornung V, Einsle O, Perner S, Imhof A, Jung M, Schule R", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31061526", "url": "https://glygen.org/publication/PubMed/31061526" } ] }, { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31061526", "url": "https://glygen.org/publication/PubMed/31061526", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AACTLETARCNKVHIQPVIT", "down_seq": "LVKGLLPRLTEKVDLLVFNP", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolished protein N(5)-glutamine methyltransferase activity. Abolished histone-lysine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31061526", "url": "https://glygen.org/publication/PubMed/31061526" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9Y5N5-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9Y5N5-1.108.108", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9Y5N5-1.122.122", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9Y5N5-1.122.125", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9Y5N5-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "ETARCNKVHIQPVITDLVKG", "down_seq": "LPRLTEKVDLLVFNPPYVVT", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Strongly reduced protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9Y5N5-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9Y5N5-1.122.122", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9Y5N5-1.122.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9Y5N5-1.125.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9Y5N5-1.128.128", "categories": [ "glycosylation_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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9Y5N5-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "KMT9 monomethylates histone H4 lysine 12 and controls proliferation of prostate cancer cells.", "journal": "Nature structural & molecular biology", "date": "2019", "authors": "Metzger E, Wang S, Urban S, Willmann D, Schmidt A, Offermann A, Allen A, Sum M, Obier N, Cottard F, Ulferts S, Preca BT, Hermann B, Maurer J, Greschik H, Hornung V, Einsle O, Perner S, Imhof A, Jung M, Schule R", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31061526", "url": "https://glygen.org/publication/PubMed/31061526" } ] }, { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31061526", "url": "https://glygen.org/publication/PubMed/31061526", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TDLVKGLLPRLTEKVDLLVF", "down_seq": "PPYVVTPPQEVGSHGIEAAW", "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "Abolished protein N(5)-glutamine methyltransferase activity. Abolished histone-lysine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31061526", "url": "https://glygen.org/publication/PubMed/31061526" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9Y5N5-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9Y5N5-1.108.108", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q9Y5N5-1.122.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9Y5N5-1.125.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9Y5N5-1.128.128", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9Y5N5-1.132.132", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9Y5N5-1.139.139", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9Y5N5-1.122.125", "start_pos": 122, "end_pos": 125, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "N(6)-Methyladenine DNA Modification in the Human Genome.", "journal": "Molecular cell", "date": "2018", "authors": "Xiao CL, Zhu S, He M, Chen, Zhang Q, Chen Y, Yu G, Liu J, Xie SQ, Luo F, Liang Z, Wang DP, Bo XC, Gu XF, Wang K, Yan GR", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "30017583", "url": "https://glygen.org/publication/PubMed/30017583" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30017583", "url": "https://glygen.org/publication/PubMed/30017583", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "NPPY", "start_aa": "N", "up_seq": "TDLVKGLLPRLTEKVDLLVF", "down_seq": "VVTPPQEVGSHGIEAAWAGG", "mutagenesis": [ { "sequence_org": "NPPY", "sequence_mut": "AAAA", "comment": "Abolished DNA methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "30017583", "url": "https://glygen.org/publication/PubMed/30017583" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9Y5N5-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9Y5N5-1.108.108", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q9Y5N5-1.122.122", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q9Y5N5-1.125.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9Y5N5-1.128.128", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9Y5N5-1.132.132", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9Y5N5-1.139.139", "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": "Q9Y5N5-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "KMT9 monomethylates histone H4 lysine 12 and controls proliferation of prostate cancer cells.", "journal": "Nature structural & molecular biology", "date": "2019", "authors": "Metzger E, Wang S, Urban S, Willmann D, Schmidt A, Offermann A, Allen A, Sum M, Obier N, Cottard F, Ulferts S, Preca BT, Hermann B, Maurer J, Greschik H, Hornung V, Einsle O, Perner S, Imhof A, Jung M, Schule R", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31061526", "url": "https://glygen.org/publication/PubMed/31061526" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31061526", "url": "https://glygen.org/publication/PubMed/31061526", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VKGLLPRLTEKVDLLVFNPP", "down_seq": "VVTPPQEVGSHGIEAAWAGG", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Abolished protein N(5)-glutamine methyltransferase activity without affecting histone-lysine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31061526", "url": "https://glygen.org/publication/PubMed/31061526" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9Y5N5-1.108.108", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9Y5N5-1.122.122", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q9Y5N5-1.122.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9Y5N5-1.128.128", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9Y5N5-1.132.132", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9Y5N5-1.139.139", "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": "Q9Y5N5-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LTEKVDLLVFNPPYVVTPPQ", "down_seq": "VGSHGIEAAWAGGRNGREVM", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Abolished protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9Y5N5-1.122.122", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9Y5N5-1.122.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9Y5N5-1.125.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9Y5N5-1.128.128", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9Y5N5-1.139.139", "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": "Q9Y5N5-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LVFNPPYVVTPPQEVGSHGI", "down_seq": "AAWAGGRNGREVMDRFFPLV", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Reduced protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9Y5N5-1.122.122", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9Y5N5-1.122.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9Y5N5-1.125.125", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9Y5N5-1.128.128", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9Y5N5-1.132.132", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9Y5N5-1.154.154", "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": "Q9Y5N5-1.154.154", "start_pos": 154, "end_pos": 154, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GSHGIEAAWAGGRNGREVMD", "down_seq": "FFPLVPDLLSPRGLFYLVTI", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Slightly reduced protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9Y5N5-1.139.139", "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": "Q9Y5N5-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "FPLVPDLLSPRGLFYLVTIK", "down_seq": "NNPEEILKIMKTKGLQGTTA", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Abolished protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q9Y5N5-1.179.179", "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": "Q9Y5N5-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KIMKTKGLQGTTALSRQAGQ", "down_seq": "TLSVLKFTKS", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Abolished protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q9Y5N5-1.210.210", "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": "Q9Y5N5-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ENFATPFHGHVGRGAFSDVY", "down_seq": "PAEDTFLLLDALEAAAAELA", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Reduced protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9Y5N5-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9Y5N5-1.27.27", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9Y5N5-1.28.28", "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": "Q9Y5N5-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ATPFHGHVGRGAFSDVYEPA", "down_seq": "DTFLLLDALEAAAAELAGVE", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Abolished protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9Y5N5-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9Y5N5-1.24.24", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9Y5N5-1.28.28", "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": "Q9Y5N5-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TPFHGHVGRGAFSDVYEPAE", "down_seq": "TFLLLDALEAAAAELAGVEI", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "N", "comment": "Abolished protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q9Y5N5-1.24.24", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9Y5N5-1.27.27", "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": "Q9Y5N5-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LLLDALEAAAAELAGVEICL", "down_seq": "VGSGSGVVSAFLASMIGPQA", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Abolished protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "Q9Y5N5-1.70.70", "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": "Q9Y5N5-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VGSGSGVVSAFLASMIGPQA", "down_seq": "YMCTDINPEAAACTLETARC", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Strongly reduced protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9Y5N5-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9Y5N5-1.77.77", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9Y5N5-1.78.78", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9Y5N5-1.83.83", "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": "Q9Y5N5-1.77.77", "start_pos": 77, "end_pos": 77, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GVVSAFLASMIGPQALYMCT", "down_seq": "INPEAAACTLETARCNKVHI", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolished protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9Y5N5-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9Y5N5-1.72.72", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9Y5N5-1.78.78", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9Y5N5-1.83.83", "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": "Q9Y5N5-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "VVSAFLASMIGPQALYMCTD", "down_seq": "NPEAAACTLETARCNKVHIQ", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "A", "comment": "Abolished protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9Y5N5-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9Y5N5-1.72.72", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9Y5N5-1.77.77", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9Y5N5-1.83.83", "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": "Q9Y5N5-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.", "journal": "Cell discovery", "date": "2019", "authors": "Li W, Shi Y, Zhang T, Ye J, Ding J", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "reference": [ { "type": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "crossref": [ { "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LASMIGPQALYMCTDINPEA", "down_seq": "ACTLETARCNKVHIQPVITD", "mutagenesis": [ { "sequence_org": "A", "sequence_mut": "D", "comment": "Strongly reduced protein N(5)-glutamine methyltransferase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" }, { "database": "PubMed", "id": "31636962", "url": "https://glygen.org/publication/PubMed/31636962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9Y5N5-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9Y5N5-1.72.72", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9Y5N5-1.77.77", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9Y5N5-1.78.78", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9Y5N5-1.103.103", "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": "Q9Y5N5-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y5N5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y5N5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VPDLLSPRGLFYLVTIKENN", "down_seq": "EEILKIMKTKGLQGTTALSR", "snv": [ { "evidence": [ { "id": "Q9Y5N5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y5N5" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNP->NNT).", "chr_id": "21", "chr_pos": "28878195", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P179", "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": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q9Y5N5-1.176.176", "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": "Q9Y5N5-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y5N5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y5N5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GLQGTTALSRQAGQETLSVL", "down_seq": "FTKS", "snv": [ { "evidence": [ { "id": "Q9Y5N5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y5N5" } ], "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 (KFT->NFT).", "chr_id": "21", "chr_pos": "28876400", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K210", "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": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9Y5N5-1.204.204", "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": "Q9Y5N5-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y5N5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y5N5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LEVGSGSGVVSAFLASMIGP", "down_seq": "ALYMCTDINPEAAACTLETA", "snv": [ { "evidence": [ { "id": "Q9Y5N5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y5N5" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "21", "chr_pos": "28882998", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q70", "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: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": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9Y5N5-1.51.51", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9Y5N5-1.72.72", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9Y5N5-1.77.77", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9Y5N5-1.78.78", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9Y5N5-1.83.83", "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": "Q9Y5N5-1.7.7", "start_pos": 7, "end_pos": 7, "uniprot_canonical_ac": "Q9Y5N5-1", "length": 214, "uniprot_id": "HEMK2_HUMAN", "protein_name": "Methyltransferase HEMK2", "refseq_ac": "NP_037372", "refseq_name": "methyltransferase HEMK2 isoform 1", "gene_name": "HEMK2", "gene_names_uniprotkb": "HEMK2; C21orf127; KMT9; N6AMT1; PRED28", "gene_names_refseq": "C21orf127; HEMK2; KMT9; MTQ2; N6AMT1; N6AMT; PRED28; PrmC; m.HsaHemK2P", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y5N5", "url": "https://www.uniprot.org/uniprotkb/Q9Y5N5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs199505140", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199505140", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199505140", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199505140", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199505140", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199505140", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199505140", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199505140#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199505140", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199505140", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MAGENF", "down_seq": "TPFHGHVGRGAFSDVYEPAE", "snv": [ { "evidence": [ { "id": "rs199505140", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199505140" }, { "id": "rs199505140", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199505140" }, { "id": "rs199505140", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199505140" }, { "id": "rs199505140", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199505140#frequency_tab" }, { "id": "rs199505140", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199505140" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFA->NFT).", "chr_id": "21", "chr_pos": "28885327", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "A7", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "128", "end_pos": "128" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "122", "end_pos": "125" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "7", "end_pos": "7" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q9Y5N5-1.24.24", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9Y5N5-1.27.27", "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": "P0DMV9-1.417.417", "start_pos": 417, "end_pos": 417, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "GlyConnect", "id": "1296", "url": "https://glyconnect.expasy.org/browser/proteins/1296" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] } ], "crossref": [ { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1296", "url": "https://glyconnect.expasy.org/browser/proteins/1296", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "APLSLGLETAGGVMTALIKR", "down_seq": "STIPTKQTQIFTTYSDNQPG", "glycosylation": [ { "glytoucan_ac": "G82830MN", "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": "Asn417", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1296", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1296" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P0DMV9-1.425.425", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P0DMV9-1.432.432", "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": 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": "P0DMV9-1.425.425", "start_pos": 425, "end_pos": 425, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P0DMV9", "url": "https://oglcnac.org/atlas/detail/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] } ], "crossref": [ { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P0DMV9", "url": "https://oglcnac.org/atlas/detail/P0DMV9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1463772783", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1463772783", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1463772783", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1463772783", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1001260474", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1001260474", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1001260474", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1001260474", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TAGGVMTALIKRNSTIPTKQ", "down_seq": "QIFTTYSDNQPGVLIQVYEG", "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": "Thr425", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "P0DMV9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P0DMV9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1463772783", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1463772783" }, { "id": "rs1463772783", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1463772783" } ], "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": "6", "chr_pos": "31829223", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T425", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1001260474", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1001260474" }, { "id": "rs1001260474", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1001260474" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "6", "chr_pos": "31829224", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T425", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P0DMV9-1.417.417", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P0DMV9-1.432.432", "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": 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": "P0DMV9-1.432.432", "start_pos": 432, "end_pos": 432, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P0DMV9", "url": "https://oglcnac.org/atlas/detail/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] } ], "crossref": [ { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P0DMV9", "url": "https://oglcnac.org/atlas/detail/P0DMV9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALIKRNSTIPTKQTQIFTTY", "down_seq": "DNQPGVLIQVYEGERAMTKD", "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": "Ser432", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "P0DMV9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P0DMV9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P0DMV9-1.417.417", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P0DMV9-1.425.425", "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": "P0DMV9-1.636.636", "start_pos": 636, "end_pos": 636, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "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": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "iPTMnet", "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs756527041", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756527041", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756527041", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756527041", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756527041", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756527041", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1816908434", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1816908434", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1816908434", "url": "https://www.ensembl.org/id/rs1816908434", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P0DMV9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0DMV9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GPGPGGFGAQGPKGGSGSGP", "down_seq": "IEEVD", "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": "Thr636", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs756527041", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756527041" }, { "id": "rs756527041", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756527041" }, { "id": "rs756527041", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756527041" } ], "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": "6", "chr_pos": "31829856", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T636", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1816908434", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1816908434" }, { "id": "rs1816908434", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1816908434" } ], "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": "6", "chr_pos": "31829857", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T636", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P0DMV9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0DMV9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "6", "chr_pos": "31829857", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T636", "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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9" } ], "site_lbl": "Thr636" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P0DMV9-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P0DMV9-1.633.633", "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": 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": 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", "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": "P0DMV9-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Combinatorial regulation of hepatic cytoplasmic signaling and nuclear transcriptional events by the OGT/REV-ERBalpha complex.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2018", "authors": "Berthier A, Vinod M, Porez G, Steenackers A, Alexandre J, Yamakawa N, Gheeraert C, Ploton M, Marechal X, Dubois-Chevalier J, Hovasse A, Schaeffer-Reiss C, Cianferani S, Rolando C, Bray F, Duez H, Eeckhoute J, Lefebvre T, Staels B, Lefebvre P", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "30397120", "url": "https://glygen.org/publication/PubMed/30397120" } ] }, { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "Identification of new O-GlcNAc modified proteins using a click-chemistry-based tagging.", "journal": "Analytical and bioanalytical chemistry", "date": "2008", "authors": "Gurcel C, Vercoutter-Edouart AS, Fonbonne C, Mortuaire M, Salvador A, Michalski JC, Lemoine J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "18369606", "url": "https://glygen.org/publication/PubMed/18369606" } ] }, { "title": "Characterization of O-GlcNAc cycling and proteomic identification of differentially O-GlcNAcylated proteins during G1/S transition.", "journal": "Biochimica et biophysica acta", "date": "2012", "authors": "Drougat L, Olivier-Van Stichelen S, Mortuaire M, Foulquier F, Lacoste AS, Michalski JC, Lefebvre T, Vercoutter-Edouart AS", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "22967762", "url": "https://glygen.org/publication/PubMed/22967762" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "Glycopeptide-specific monoclonal antibodies suggest new roles for O-GlcNAc.", "journal": "Nature chemical biology", "date": "2010", "authors": "Teo CF, Ingale S, Wolfert MA, Elsayed GA, Not LG, Chatham JC, Wells L, Boons GJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "20305658", "url": "https://glygen.org/publication/PubMed/20305658" } ] }, { "title": "O-GlcNAcylation promotes fatty acid synthase activity under nutritional stress as a pro-survival mechanism in cancer cells.", "journal": "Proteomics", "date": "2022", "authors": "Wong YK, Wang J, Lim TK, Lin Q, Yap CT, Shen HM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Elevated O-GlcNAcylation of Extracellular Vesicle Proteins Derived from Metastatic Colorectal Cancer Cells.", "journal": "Cancer genomics & proteomics", "date": "2016", "authors": "Chaiyawat P, Weeraphan C, Netsirisawan P, Chokchaichamnankit D, Srisomsap C, Svasti J, Champattanachai V", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "27566657", "url": "https://glygen.org/publication/PubMed/27566657" } ] }, { "title": "Z-band alternatively spliced PDZ motif protein (ZASP) is the major O-linked beta-N-acetylglucosamine-substituted protein in human heart myofibrils.", "journal": "The Journal of biological chemistry", "date": "2013", "authors": "Leung MC, Hitchen PG, Ward DG, Messer AE, Marston SB", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "23271734", "url": "https://glygen.org/publication/PubMed/23271734" } ] }, { "title": "70-kDa-heat shock protein presents an adjustable lectinic activity towards O-linked N-acetylglucosamine.", "journal": "Biochemical and biophysical research communications", "date": "2004", "authors": "Guinez C, Lemoine J, Michalski JC, Lefebvre T", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "15158436", "url": "https://glygen.org/publication/PubMed/15158436" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P0DMV9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30397120", "url": "https://glygen.org/publication/PubMed/30397120", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18369606", "url": "https://glygen.org/publication/PubMed/18369606", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22967762", "url": "https://glygen.org/publication/PubMed/22967762", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20305658", "url": "https://glygen.org/publication/PubMed/20305658", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27566657", "url": "https://glygen.org/publication/PubMed/27566657", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23271734", "url": "https://glygen.org/publication/PubMed/23271734", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15158436", "url": "https://glygen.org/publication/PubMed/15158436", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "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": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "P0DMV9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P0DMV9" }, { "id": "30397120", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30397120" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "18369606", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/18369606" }, { "id": "22967762", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22967762" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "20305658", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20305658" }, { "id": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "27566657", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27566657" }, { "id": "23271734", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23271734" }, { "id": "15158436", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/15158436" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P0DMV9-1.10.10", "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": 15 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P0DMV9-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Biochemical and structural studies on the high affinity of Hsp70 for ADP.", "journal": "Protein science : a publication of the Protein Society", "date": "2011", "authors": "Arakawa A, Handa N, Shirouzu M, Yokoyama S", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "21608060", "url": "https://glygen.org/publication/PubMed/21608060" } ] } ], "crossref": [ { "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21608060", "url": "https://glygen.org/publication/PubMed/21608060", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MAKAAAIGI", "down_seq": "LGTTYSCVGVFQHGKVEIIA", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Reduces affinity for ADP.", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "PubMed", "id": "21608060", "url": "https://glygen.org/publication/PubMed/21608060" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P0DMV9-1.0.0", "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": "P0DMV9-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Biochemical and structural studies on the high affinity of Hsp70 for ADP.", "journal": "Protein science : a publication of the Protein Society", "date": "2011", "authors": "Arakawa A, Handa N, Shirouzu M, Yokoyama S", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "21608060", "url": "https://glygen.org/publication/PubMed/21608060" } ] } ], "crossref": [ { "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21608060", "url": "https://glygen.org/publication/PubMed/21608060", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AAIAYGLDRTGKGERNVLIF", "down_seq": "LGGGTFDVSILTIDDGIFEV", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Reduces affinity for ADP.", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "PubMed", "id": "21608060", "url": "https://glygen.org/publication/PubMed/21608060" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": "P0DMV9-1.561.561", "start_pos": 561, "end_pos": 561, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity.", "journal": "PLoS genetics", "date": "2013", "authors": "Cloutier P, Lavallee-Adam M, Faubert D, Blanchette M, Coulombe B", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "23349634", "url": "https://glygen.org/publication/PubMed/23349634" } ] }, { "title": "Identification and characterization of a novel human methyltransferase modulating Hsp70 protein function through lysine methylation.", "journal": "The Journal of biological chemistry", "date": "2013", "authors": "Jakobsson ME, Moen A, Bousset L, Egge-Jacobsen W, Kernstock S, Melki R, Falnes PO", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "23921388", "url": "https://glygen.org/publication/PubMed/23921388" } ] } ], "crossref": [ { "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23349634", "url": "https://glygen.org/publication/PubMed/23349634", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23921388", "url": "https://glygen.org/publication/PubMed/23921388", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ALESYAFNMKSAVEDEGLKG", "down_seq": "ISEADKKKVLDKCQEVISWL", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Complete loss of in vitro methylation by METTL21A.", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "PubMed", "id": "23349634", "url": "https://glygen.org/publication/PubMed/23349634" }, { "database": "PubMed", "id": "23921388", "url": "https://glygen.org/publication/PubMed/23921388" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P0DMV9-1.77.77", "start_pos": 77, "end_pos": 77, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ARD1-mediated Hsp70 acetylation balances stress-induced protein refolding and degradation.", "journal": "Nature communications", "date": "2016", "authors": "Seo JH, Park JH, Lee EJ, Vo TT, Choi H, Kim JY, Jang JK, Wee HJ, Lee HS, Jang SH, Park ZY, Jeong J, Lee KJ, Seok SH, Park JY, Lee BJ, Lee MN, Oh GT, Kim KW", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "27708256", "url": "https://glygen.org/publication/PubMed/27708256" } ] } ], "crossref": [ { "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "27708256", "url": "https://glygen.org/publication/PubMed/27708256", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NQVALNPQNTVFDAKRLIGR", "down_seq": "FGDPVVQSDMKHWPFQVIND", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "Q", "comment": "No loss of acetylation and ATPase activity. Exhibits normal protein refolding activity during the early phase but exhibits defects in ubiquitin-mediated protein degradation during the later phase.", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "PubMed", "id": "27708256", "url": "https://glygen.org/publication/PubMed/27708256" } ] }, { "sequence_org": "K", "sequence_mut": "R", "comment": "Significant loss of acetylation and ATPase activity. Decreased binding to HOPX and HSP90 and increased binding to STUB1 and NAA10. Impaired capacity for protein refolding during the early phase after stress but shows normal protein degradation activity in the late phase.", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "PubMed", "id": "27708256", "url": "https://glygen.org/publication/PubMed/27708256" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P0DMV9-1.66.66", "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": "P0DMV9-1.631.631", "start_pos": 631, "end_pos": 631, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "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": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "iPTMnet", "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YQGAGGPGPGGFGAQGPKGG", "down_seq": "GSGPTIEEVD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9" } ], "site_lbl": "Ser631" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P0DMV9-1.633.633", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P0DMV9-1.636.636", "categories": [ "glycosylation_flag", "snv_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": "P0DMV9-1.633.633", "start_pos": 633, "end_pos": 633, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "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": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "iPTMnet", "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAGGPGPGGFGAQGPKGGSG", "down_seq": "GPTIEEVD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9" } ], "site_lbl": "Ser633" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P0DMV9-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P0DMV9-1.636.636", "categories": [ "glycosylation_flag", "snv_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": "P0DMV9-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "P0DMV9-1", "length": 641, "uniprot_id": "HS71B_HUMAN", "protein_name": "Heat shock 70 kDa protein 1B", "refseq_ac": "NP_005337", "refseq_name": "heat shock 70 kDa protein 1B", "gene_name": "HSPA1B", "gene_names_uniprotkb": "HSPA1B; HSP72", "gene_names_refseq": "HSP70-1B; HSP70-1; HSP70-2; HSP70.1; HSP70.2; HSP72; HSPA1B; HSPA1; HSX70", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0DMV9", "url": "https://www.uniprot.org/uniprotkb/P0DMV9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Hsp72 is targeted to the mitotic spindle by Nek6 to promote K-fiber assembly and mitotic progression.", "journal": "The Journal of cell biology", "date": "2015", "authors": "O'Regan L, Sampson J, Richards MW, Knebel A, Roth D, Hood FE, Straube A, Royle SJ, Bayliss R, Fry AM", "evidence": [ { "database": "iPTMnet", "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9" } ], "reference": [ { "type": "PubMed", "id": "25940345", "url": "https://glygen.org/publication/PubMed/25940345" } ] } ], "crossref": [ { "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "25940345", "url": "https://glygen.org/publication/PubMed/25940345", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DTERLIGDAAKNQVALNPQN", "down_seq": "VFDAKRLIGRKFGDPVVQSD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P0DMV9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P0DMV9" }, { "database": "PubMed", "id": "25940345", "url": "https://glygen.org/publication/PubMed/25940345" } ], "site_lbl": "Thr66" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "snv", "site_list": [ { "start_pos": "425", "end_pos": "425" }, { "start_pos": "636", "end_pos": "636" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "631", "end_pos": "631" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "P0DMV9-1.77.77", "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": "O95757-1.769.769", "start_pos": 769, "end_pos": 769, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "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": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "Tandem Bioorthogonal Labeling Uncovers Endogenous Cotranslationally O-GlcNAc Modified Nascent Proteins.", "journal": "Journal of the American Chemical Society", "date": "2020", "authors": "Zhu Y, Willems LI, Salas D, Cecioni S, Wu WB, Foster LJ, Vocadlo DJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" } ], "reference": [ { "type": "PubMed", "id": "32870666", "url": "https://glygen.org/publication/PubMed/32870666" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" } ], "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": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" } ], "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": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" }, { "database": "O-GlcNAc Atlas", "id": "O95757", "url": "https://oglcnac.org/atlas/detail/O95757" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95757", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "32870666", "url": "https://glygen.org/publication/PubMed/32870666", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "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": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95757", "url": "https://oglcnac.org/atlas/detail/O95757", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O95757", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSKMNAQNKLSLTQDPVVKV", "down_seq": "EIVAKSKELDNFCNPIIYKP", "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": "Ser769", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "O95757", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95757" }, { "id": "32870666", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32870666" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "O95757", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O95757" } ] } ], "snv": [ { "evidence": [ { "id": "O95757", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "4", "chr_pos": "127830777", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S769", "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: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": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "O95757-1.761.761", "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": 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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95757-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95757", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MSVVGIDLGFLNC", "down_seq": "IAVARSGGIETIANEYSDRC", "snv": [ { "evidence": [ { "id": "O95757", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757" } ], "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 (NCY->NCC).", "chr_id": "4", "chr_pos": "127782591", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Y14", "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": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "O95757-1.32.32", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "O95757-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs573754238", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs573754238", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs573754238", "url": "http://gnomad.broadinstitute.org/awesome?query=rs573754238", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "FTDAERRSVMAAAQVAGLNC", "down_seq": "RLMNETTAVALAYGIYKQDL", "snv": [ { "evidence": [ { "id": "rs573754238", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs573754238" }, { "id": "rs573754238", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs573754238" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCL->NCS).", "chr_id": "4", "chr_pos": "127801211", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L168", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "O95757-1.171.171", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95757-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95757", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "AERRSVMAAAQVAGLNCLRL", "down_seq": "NETTAVALAYGIYKQDLPPL", "snv": [ { "evidence": [ { "id": "O95757", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "127801221", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "M171", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O95757-1.168.168", "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": "O95757-1.211.211", "start_pos": 211, "end_pos": 211, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95757", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LDEKPRNVVFIDMGHSAYQV", "down_seq": "VCAFNKGKLKVLATTFDPYL", "snv": [ { "evidence": [ { "id": "O95757", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "127801887", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L211", "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: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": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "O95757-1.230.230", "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": "O95757-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761233683", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761233683", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761233683", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761233683", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761233683", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761233683", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LPLNIECFMNDLDVSSKMNR", "down_seq": "QFEQLCASLLARVEPPLKAV", "snv": [ { "evidence": [ { "id": "rs761233683", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761233683" }, { "id": "rs761233683", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761233683" }, { "id": "rs761233683", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761233683" } ], "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": "4", "chr_pos": "127804012", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A304", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "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": "O95757-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs546264952", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs546264952", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs546264952", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs546264952", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs546264952", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs546264952", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs546264952", "url": "http://gnomad.broadinstitute.org/awesome?query=rs546264952", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NCYIAVARSGGIETIANEYS", "down_seq": "RCTPACISLGSRTRAIGNAA", "snv": [ { "evidence": [ { "id": "rs546264952", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs546264952" }, { "id": "rs546264952", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs546264952" }, { "id": "rs546264952", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs546264952" }, { "id": "rs546264952", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs546264952" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DRC->NRC).", "chr_id": "4", "chr_pos": "127782644", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "D32", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O95757-1.14.14", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95757-1.381.381", "start_pos": 381, "end_pos": 381, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95757", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DISTTLNADEAVARGCALQC", "down_seq": "ILSPAFKVREFSITDLVPYS", "snv": [ { "evidence": [ { "id": "O95757", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "127805691", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A381", "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: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": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "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": "O95757-1.425.425", "start_pos": 425, "end_pos": 425, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs139612462", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139612462", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs139612462", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139612462", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs139612462", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139612462#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs139612462", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139612462", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "RWKTSFEDGSGECEVFCKNH", "down_seq": "APFSKVITFHKKEPFELEAF", "snv": [ { "evidence": [ { "id": "rs139612462", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139612462" }, { "id": "rs139612462", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139612462" }, { "id": "rs139612462", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139612462#frequency_tab" }, { "id": "rs139612462", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139612462" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHP->NHS).", "chr_id": "4", "chr_pos": "127808024", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P425", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "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": "O95757-1.474.474", "start_pos": 474, "end_pos": 474, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95757", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "YPDARIGSFTIQNVFPQSDG", "down_seq": "SSKVKVKVRVNIHGIFSVAS", "snv": [ { "evidence": [ { "id": "O95757", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4177", "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": "4", "chr_pos": "127811478", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D474", "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": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "O95757-1.483.483", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O95757-1.494.494", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "O95757-1.483.483", "start_pos": 483, "end_pos": 483, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95757", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TIQNVFPQSDGDSSKVKVKV", "down_seq": "VNIHGIFSVASASVIEKQNL", "snv": [ { "evidence": [ { "id": "O95757", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757" } ], "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 (4).", "chr_id": "4", "chr_pos": "127811505", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R483", "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: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": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O95757-1.474.474", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O95757-1.494.494", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "O95757-1.494.494", "start_pos": 494, "end_pos": 494, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs558522972", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558522972", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs558522972", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs558522972", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs558522972", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558522972", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs558522972", "url": "http://gnomad.broadinstitute.org/awesome?query=rs558522972", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DSSKVKVKVRVNIHGIFSVA", "down_seq": "ASVIEKQNLEGDHSDAPMET", "snv": [ { "evidence": [ { "id": "rs558522972", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558522972" }, { "id": "rs558522972", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs558522972" }, { "id": "rs558522972", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558522972" }, { "id": "rs558522972", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs558522972" } ], "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": "4", "chr_pos": "127811539", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S494", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O95757-1.474.474", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "O95757-1.483.483", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O95757-1.506.506", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O95757-1.508.508", "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": "O95757-1.506.506", "start_pos": 506, "end_pos": 506, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs151328982", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs151328982", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs151328982", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs151328982", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs151328982", "url": "https://www.ncbi.nlm.nih.gov/snp/rs151328982#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs151328982", "url": "http://gnomad.broadinstitute.org/awesome?query=rs151328982", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "IHGIFSVASASVIEKQNLEG", "down_seq": "HSDAPMETETSFKNENKDNM", "snv": [ { "evidence": [ { "id": "rs151328982", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs151328982" }, { "id": "rs151328982", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs151328982" }, { "id": "rs151328982", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs151328982#frequency_tab" }, { "id": "rs151328982", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs151328982" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DHS->NHS).", "chr_id": "4", "chr_pos": "127811574", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D506", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O95757-1.494.494", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O95757-1.508.508", "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": "O95757-1.600.600", "start_pos": 600, "end_pos": 600, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95757", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs76972854", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs76972854", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs76972854", "url": "https://www.ensembl.org/id/rs76972854", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "IDLPIQSSLCRQLGQDLLNS", "down_seq": "IENEGKMIMQDKLEKERNDA", "snv": [ { "evidence": [ { "id": "O95757", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95757" }, { "id": "rs76972854", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs76972854" }, { "id": "rs76972854", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs76972854" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Y", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSY->NSC).", "chr_id": "4", "chr_pos": "127820552", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Y600", "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": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O95757-1.599.599", "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": "O95757-1.705.705", "start_pos": 705, "end_pos": 705, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs755721610", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755721610", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755721610", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755721610", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755721610", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755721610", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "GQPIQMKYMEHEERPKALND", "down_seq": "GKKIQLVMKVIEAYRNKDER", "snv": [ { "evidence": [ { "id": "rs755721610", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755721610" }, { "id": "rs755721610", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755721610" }, { "id": "rs755721610", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755721610" } ], "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": "127827372", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L705", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O95757-1.692.692", "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": "O95757-1.230.230", "start_pos": 230, "end_pos": 230, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "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": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VLVCAFNKGKLKVLATTFDP", "down_seq": "LGGRNFDEALVDYFCDEFKT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr230" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O95757-1.211.211", "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": "O95757-1.508.508", "start_pos": 508, "end_pos": 508, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "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": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" }, { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GIFSVASASVIEKQNLEGDH", "down_seq": "DAPMETETSFKNENKDNMDK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "site_lbl": "Ser508" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O95757-1.494.494", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O95757-1.506.506", "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": "O95757-1.545.545", "start_pos": 545, "end_pos": 545, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NMDKMQVDQEEGHQKCHAEH", "down_seq": "PEEEIDHTGAKTKSAVSDKQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "site_lbl": "Thr545" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "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": "O95757-1.571.571", "start_pos": 571, "end_pos": 571, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008", "authors": "McNulty DE, Annan RS", "evidence": [ { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "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": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DHTGAKTKSAVSDKQDRLNQ", "down_seq": "LKKGKVKSIDLPIQSSLCRQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Thr571" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "O95757-1.579.579", "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": "O95757-1.579.579", "start_pos": 579, "end_pos": 579, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "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": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" }, { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SAVSDKQDRLNQTLKKGKVK", "down_seq": "IDLPIQSSLCRQLGQDLLNS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "site_lbl": "Ser579" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "O95757-1.571.571", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O95757-1.599.599", "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": "O95757-1.599.599", "start_pos": 599, "end_pos": 599, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "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": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757", "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": "SIDLPIQSSLCRQLGQDLLN", "down_seq": "YIENEGKMIMQDKLEKERND", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser599" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O95757-1.579.579", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O95757-1.600.600", "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": "O95757-1.684.684", "start_pos": 684, "end_pos": 684, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "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": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "EDGEDQPKQVYVDKLQELKK", "down_seq": "GQPIQMKYMEHEERPKALND", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr684" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "O95757-1.692.692", "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": "O95757-1.692.692", "start_pos": 692, "end_pos": 692, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "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": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QVYVDKLQELKKYGQPIQMK", "down_seq": "MEHEERPKALNDLGKKIQLV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr692" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "O95757-1.684.684", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O95757-1.705.705", "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": "O95757-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "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": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" }, { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SQIVTNVRNTIHGFKKLHGR", "down_seq": "FDDPIVQTERIRLPYELQKM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "site_lbl": "Ser74" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "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": "O95757-1.761.761", "start_pos": 761, "end_pos": 761, "uniprot_canonical_ac": "O95757-1", "length": 839, "uniprot_id": "HS74L_HUMAN", "protein_name": "Heat shock 70 kDa protein 4L", "refseq_ac": "NP_001304310", "refseq_name": "heat shock 70 kDa protein 4L isoform 2", "gene_name": "HSPA4L", "gene_names_uniprotkb": "HSPA4L; APG1; HSPH3; OSP94", "gene_names_refseq": "APG-1; APG1; HSPA4L; HSPH3; Osp94", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.", "journal": "Science (New York, N.Y.)", "date": "2007", "authors": "Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ", "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" }, { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] } ], "crossref": [ { "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ISDAMSWLNSKMNAQNKLSL", "down_seq": "QDPVVKVSEIVAKSKELDNF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O95757", "url": "https://www.uniprot.org/uniprotkb/O95757" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "iPTMnet", "id": "O95757", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95757" } ], "site_lbl": "Thr761" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "769", "end_pos": "769" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "769", "end_pos": "769" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "761", "end_pos": "761" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "O95757-1.769.769", "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": "P22692-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "P22692-1", "length": 258, "uniprot_id": "IBP4_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 4", "refseq_ac": "NP_001543", "refseq_name": "insulin-like growth factor-binding protein 4 precursor", "gene_name": "IGFBP4", "gene_names_uniprotkb": "IGFBP4; IBP4", "gene_names_refseq": "BP-4; HT29-IGFBP; IBP4; IGFBP-4; IGFBP4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification and molecular cloning of two new 30-kDa insulin-like growth factor binding proteins isolated from adult human serum.", "journal": "The Journal of biological chemistry", "date": "1991", "authors": "Kiefer MC, Masiarz FR, Bauer DM, Zapf J", "evidence": [ { "database": "UniProtKB", "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692#ptm_processing" }, { "database": "UniProtKB", "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692" } ], "reference": [ { "type": "PubMed", "id": "1709161", "url": "https://glygen.org/publication/PubMed/1709161" } ] } ], "crossref": [ { "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "1709161", "url": "https://glygen.org/publication/PubMed/1709161", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs143445546", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143445546", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143445546", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143445546", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs143445546", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143445546", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs143445546", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143445546#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143445546", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143445546", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EIEAIQESLQPSDKDEGDHP", "down_seq": "NSFSPCSAHDRRCLQKHFAK", "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": "Asn125", "evidence": [ { "id": "P22692", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P22692#ptm_processing" }, { "id": "1709161", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/1709161" } ] } ], "snv": [ { "evidence": [ { "id": "rs143445546", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143445546" }, { "id": "rs143445546", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143445546" }, { "id": "rs143445546", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143445546" }, { "id": "rs143445546", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143445546#frequency_tab" }, { "id": "rs143445546", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143445546" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NNS->KNS).", "chr_id": "17", "chr_pos": "40453010", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "N125", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "164", "end_pos": "180" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "snv", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P22692-1.127.127", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P22692-1.164.180", "start_pos": 164, "end_pos": 180, "uniprot_canonical_ac": "P22692-1", "length": 258, "uniprot_id": "IBP4_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 4", "refseq_ac": "NP_001543", "refseq_name": "insulin-like growth factor-binding protein 4 precursor", "gene_name": "IGFBP4", "gene_names_uniprotkb": "IGFBP4; IBP4", "gene_names_refseq": "BP-4; HT29-IGFBP; IBP4; IGFBP-4; IGFBP4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692" } ], "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": "EDARPVPQGSCQSELHR", "start_aa": "E", "up_seq": "AKIRDRSTSGGKMKVNGAPR", "down_seq": "ALERLAASQSRTHEDLYIIP", "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": "EDARPVPQGSCQSELHR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Glu", "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": "125", "end_pos": "125" }, { "start_pos": "164", "end_pos": "180" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "snv", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P22692-1.173.173", "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" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 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": "P22692-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "P22692-1", "length": 258, "uniprot_id": "IBP4_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 4", "refseq_ac": "NP_001543", "refseq_name": "insulin-like growth factor-binding protein 4 precursor", "gene_name": "IGFBP4", "gene_names_uniprotkb": "IGFBP4; IBP4", "gene_names_refseq": "BP-4; HT29-IGFBP; IBP4; IGFBP-4; IGFBP4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692" } ], "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" ] }, { "id": "P22692", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22692", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs762201349", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762201349", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762201349", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762201349", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762201349", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762201349", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GGKMKVNGAPREDARPVPQG", "down_seq": "CQSELHRALERLAASQSRTH", "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": "S", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser173", "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" } ] } ], "snv": [ { "evidence": [ { "id": "P22692", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P22692" }, { "id": "rs762201349", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762201349" }, { "id": "rs762201349", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762201349" }, { "id": "rs762201349", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762201349" } ], "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": "17", "chr_pos": "40453938", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S173", "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": "125", "end_pos": "125" }, { "start_pos": "164", "end_pos": "180" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "snv", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P22692-1.164.180", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P22692-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P22692-1", "length": 258, "uniprot_id": "IBP4_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 4", "refseq_ac": "NP_001543", "refseq_name": "insulin-like growth factor-binding protein 4 precursor", "gene_name": "IGFBP4", "gene_names_uniprotkb": "IGFBP4; IBP4", "gene_names_refseq": "BP-4; HT29-IGFBP; IBP4; IGFBP-4; IGFBP4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P22692", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P22692" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] } ], "crossref": [ { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P22692", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P22692", "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": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "P22692", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P22692" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "164", "end_pos": "180" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "snv", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "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": "P22692-1.127.127", "start_pos": 127, "end_pos": 127, "uniprot_canonical_ac": "P22692-1", "length": 258, "uniprot_id": "IBP4_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 4", "refseq_ac": "NP_001543", "refseq_name": "insulin-like growth factor-binding protein 4 precursor", "gene_name": "IGFBP4", "gene_names_uniprotkb": "IGFBP4; IBP4", "gene_names_refseq": "BP-4; HT29-IGFBP; IBP4; IGFBP-4; IGFBP4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1406315556", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1406315556", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1406315556", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1406315556", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EAIQESLQPSDKDEGDHPNN", "down_seq": "FSPCSAHDRRCLQKHFAKIR", "snv": [ { "evidence": [ { "id": "rs1406315556", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1406315556" }, { "id": "rs1406315556", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1406315556" } ], "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 (NNS->NNG).", "chr_id": "17", "chr_pos": "40453014", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S127", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "164", "end_pos": "180" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "snv", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P22692-1.125.125", "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": "P22692-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "P22692-1", "length": 258, "uniprot_id": "IBP4_HUMAN", "protein_name": "Insulin-like growth factor-binding protein 4", "refseq_ac": "NP_001543", "refseq_name": "insulin-like growth factor-binding protein 4 precursor", "gene_name": "IGFBP4", "gene_names_uniprotkb": "IGFBP4; IBP4", "gene_names_refseq": "BP-4; HT29-IGFBP; IBP4; IGFBP-4; IGFBP4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A Single Kinase Generates the Majority of the Secreted Phosphoproteome.", "journal": "Cell", "date": "2015", "authors": "Tagliabracci VS, Wiley SE, Guo X, Kinch LN, Durrant E, Wen J, Xiao J, Cui J, Nguyen KB, Engel JL, Coon JJ, Grishin N, Pinna LA, Pagliarini DJ, Dixon JE", "evidence": [ { "database": "UniProtKB", "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692" }, { "database": "Reactome", "id": "R-HSA-381426", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-381426" }, { "database": "iPTMnet", "id": "P22692", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P22692" } ], "reference": [ { "type": "PubMed", "id": "26091039", "url": "https://glygen.org/publication/PubMed/26091039" } ] } ], "crossref": [ { "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P22692", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P22692", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "26091039", "url": "https://glygen.org/publication/PubMed/26091039", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VKLPGGLEPKGELDCHQLAD", "down_seq": "FRE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by FAM20C", "evidence": [ { "database": "UniProtKB", "id": "P22692", "url": "https://www.uniprot.org/uniprotkb/P22692" }, { "database": "iPTMnet", "id": "P22692", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P22692" }, { "database": "PubMed", "id": "26091039", "url": "https://glygen.org/publication/PubMed/26091039" } ], "site_lbl": "Ser255" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "164", "end_pos": "180" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "snv", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "173", "end_pos": "173" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "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": "P48723-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "GlyConnect", "id": "1294", "url": "https://glyconnect.expasy.org/browser/proteins/1294" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "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": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1294", "url": "https://glyconnect.expasy.org/browser/proteins/1294", "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_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs776378274", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776378274", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776378274", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776378274", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776378274", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776378274", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GRYPFKVLNKNGMVEFSVTS", "down_seq": "ETITVSPEYVGSRLLLKLKE", "glycosylation": [ { "glytoucan_ac": "G14260UH", "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": "Asn137", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1294", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1294" } ] }, { "glytoucan_ac": "G90653XK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NGMVEFSVTSNETITVSPEYVGSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn137", "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" } ] } ], "snv": [ { "evidence": [ { "id": "rs776378274", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776378274" }, { "id": "rs776378274", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776378274" }, { "id": "rs776378274", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776378274" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NET->SET).", "chr_id": "21", "chr_pos": "14378369", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N137", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P48723-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P48723-1.139.139", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P48723-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "GlyConnect", "id": "1294", "url": "https://glyconnect.expasy.org/browser/proteins/1294" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "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" } ] }, { "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" } ] }, { "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": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1294", "url": "https://glyconnect.expasy.org/browser/proteins/1294", "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": "P48723@N184", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P48723@N184", "database": "GPTwiki", "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": "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": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1445815217", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1445815217", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1445815217", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1445815217", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GMPVANAVISVPAEFDLKQR", "down_seq": "STIEAANLAGLKILRVINEP", "glycosylation": [ { "glytoucan_ac": "G05724UK", "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": "Asn184", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1294", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1294" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nSTIEAANLAGLK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn184", "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": "QRnSTIEAANLAGLK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn184", "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": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn184", "evidence": [ { "id": "P48723@N184", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P48723@N184" }, { "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" }, { "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": "G64527OM", "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": "Asn184", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1294", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1294" } ] }, { "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": "Asn184", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1294", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1294" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QRnSTIEAANLAGLK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn184", "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": "Asn184", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "snv": [ { "evidence": [ { "id": "rs1445815217", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1445815217" }, { "id": "rs1445815217", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1445815217" } ], "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": "21", "chr_pos": "14378228", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N184", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P48723-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P48723-1.185.185", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P48723-1.186.186", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P48723-1.200.215", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P48723-1.204.204", "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": 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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P48723-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P48723", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723" } ], "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": "P48723", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "P48723", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723" }, { "database": "O-GlcNAc Atlas", "id": "P48723", "url": "https://oglcnac.org/atlas/detail/P48723" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "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": "P48723", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723" }, { "database": "O-GlcNAc Atlas", "id": "P48723", "url": "https://oglcnac.org/atlas/detail/P48723" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P48723", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P48723", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "P48723", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723" }, { "database": "O-GlcNAc Atlas", "id": "P48723", "url": "https://oglcnac.org/atlas/detail/P48723" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "P48723", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P48723", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "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": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P48723", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P48723", "url": "https://oglcnac.org/atlas/detail/P48723", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1731594348", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1731594348", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1731594348", "url": "https://www.ensembl.org/id/rs1731594348", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723", "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": "MPVANAVISVPAEFDLKQRN", "down_seq": "TIEAANLAGLKILRVINEPT", "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": "Ser185", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "P48723", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P48723" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "P48723", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P48723" } ] } ], "snv": [ { "evidence": [ { "id": "rs1731594348", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1731594348" }, { "id": "rs1731594348", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1731594348" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "21", "chr_pos": "14378225", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S185", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1731594348", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1731594348" }, { "id": "rs1731594348", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1731594348" } ], "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": "21", "chr_pos": "14378225", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S185", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser185" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P48723-1.184.184", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P48723-1.186.186", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P48723-1.200.215", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P48723-1.204.204", "categories": [ "snv_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": 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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P48723-1.200.215", "start_pos": 200, "end_pos": 215, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "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": "VINEPTAAAMAYGLHK", "start_aa": "V", "up_seq": "LKQRNSTIEAANLAGLKILR", "down_seq": "ADVFHVLVIDLGGGTLDVSL", "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": "VINEPTAAAMAYGLHK", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Val", "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": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P48723-1.184.184", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P48723-1.185.185", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P48723-1.186.186", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P48723-1.204.204", "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": "P48723-1.298.298", "start_pos": 298, "end_pos": 298, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "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": "rs769857498", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769857498", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769857498", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769857498", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769857498", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769857498", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VPSRKEEIHRLRQAVEMVKL", "down_seq": "LTLHQSAQLSVLLTVEEQDR", "glycosylation": [ { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QAVEMVKLNLTLHQSAQLSVLLTVEEQDRK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn298", "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" } ] } ], "snv": [ { "evidence": [ { "id": "rs769857498", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769857498" }, { "id": "rs769857498", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769857498" }, { "id": "rs769857498", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769857498" } ], "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": "21", "chr_pos": "14374140", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N298", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P48723-1.280.280", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P48723-1.300.300", "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": 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": "P48723-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1461327946", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1461327946", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1461327946", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1461327946#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1461327946", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1461327946", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YPFKVLNKNGMVEFSVTSNE", "down_seq": "ITVSPEYVGSRLLLKLKEMA", "snv": [ { "evidence": [ { "id": "rs1461327946", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1461327946" }, { "id": "rs1461327946", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1461327946#frequency_tab" }, { "id": "rs1461327946", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1461327946" } ], "glycoeffect": [ "n-glyco-sequon-gain", "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (TIT->NIT); n-glyco-sequon-loss (NET->NEN).", "chr_id": "21", "chr_pos": "14378363", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T139", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1461327946", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1461327946" }, { "id": "rs1461327946", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1461327946#frequency_tab" }, { "id": "rs1461327946", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1461327946" } ], "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 (NET->NEI).", "chr_id": "21", "chr_pos": "14378363", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T139", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P48723-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P48723-1.137.137", "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": "P48723-1.127.127", "start_pos": 127, "end_pos": 127, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs939679022", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs939679022", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs939679022", "url": "https://www.ncbi.nlm.nih.gov/snp/rs939679022#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs939679022", "url": "http://gnomad.broadinstitute.org/awesome?query=rs939679022", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FTAEELEAEIGRYPFKVLNK", "down_seq": "GMVEFSVTSNETITVSPEYV", "snv": [ { "evidence": [ { "id": "rs939679022", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs939679022" }, { "id": "rs939679022", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs939679022#frequency_tab" }, { "id": "rs939679022", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs939679022" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKN->NKS).", "chr_id": "21", "chr_pos": "14378399", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N127", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P48723-1.137.137", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P48723-1.139.139", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P48723-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P48723", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P48723", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PEYVGSRLLLKLKEMAEAYL", "down_seq": "MPVANAVISVPAEFDLKQRN", "snv": [ { "evidence": [ { "id": "P48723", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P48723" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "21", "chr_pos": "14378288", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G164", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "P48723-1.184.184", "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": 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": "P48723-1.186.186", "start_pos": 186, "end_pos": 186, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "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": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "rs1329386545", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1329386545", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1329386545", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1329386545", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723", "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": "PVANAVISVPAEFDLKQRNS", "down_seq": "IEAANLAGLKILRVINEPTA", "snv": [ { "evidence": [ { "id": "rs1329386545", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1329386545" }, { "id": "rs1329386545", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1329386545" } ], "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": "21", "chr_pos": "14378222", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T186", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr186" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P48723-1.184.184", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P48723-1.185.185", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P48723-1.200.215", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P48723-1.204.204", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P48723-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1369927348", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369927348", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1369927348", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1369927348#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1369927348", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369927348", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NSTIEAANLAGLKILRVINE", "down_seq": "TAAAMAYGLHKADVFHVLVI", "snv": [ { "evidence": [ { "id": "rs1369927348", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369927348" }, { "id": "rs1369927348", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1369927348#frequency_tab" }, { "id": "rs1369927348", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369927348" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEP->NES).", "chr_id": "21", "chr_pos": "14375790", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P204", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P48723-1.184.184", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P48723-1.185.185", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P48723-1.186.186", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P48723-1.200.215", "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": "P48723-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P48723", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P48723", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LGGGTLDVSLLNKQGGMFLT", "down_seq": "AMSGNNKLGGQDFNQRLLQY", "snv": [ { "evidence": [ { "id": "P48723", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P48723" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "21", "chr_pos": "14375664", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R246", "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": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P48723-1.262.262", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "P48723-1.262.262", "start_pos": 262, "end_pos": 262, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1370298596", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1370298596", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1370298596", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1370298596#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1370298596", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1370298596", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MFLTRAMSGNNKLGGQDFNQ", "down_seq": "LLQYLYKQIYQTYGFVPSRK", "snv": [ { "evidence": [ { "id": "rs1370298596", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1370298596" }, { "id": "rs1370298596", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1370298596#frequency_tab" }, { "id": "rs1370298596", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1370298596" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NQR->NQS).", "chr_id": "21", "chr_pos": "14374247", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R262", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P48723-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P48723-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P48723-1.275.275", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P48723-1.280.280", "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": "P48723-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1982895678", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1982895678", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1982895678", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1982895678#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1982895752", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1982895752", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1982895752", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1982895752#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SRKEEIHRLRQAVEMVKLNL", "down_seq": "LHQSAQLSVLLTVEEQDRKE", "snv": [ { "evidence": [ { "id": "rs1982895678", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1982895678" }, { "id": "rs1982895678", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1982895678#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 (NLT->NLI).", "chr_id": "21", "chr_pos": "14374134", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T300", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1982895752", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1982895752" }, { "id": "rs1982895752", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1982895752#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLP).", "chr_id": "21", "chr_pos": "14374135", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T300", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P48723-1.280.280", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P48723-1.298.298", "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": "P48723-1.471.471", "start_pos": 471, "end_pos": 471, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1982880189", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1982880189", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1982880189", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1982880189#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "WPLQVSALEIPNKHLQKTNF", "down_seq": "", "snv": [ { "evidence": [ { "id": "rs1982880189", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1982880189" }, { "id": "rs1982880189", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1982880189#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFN->NFS).", "chr_id": "21", "chr_pos": "14373621", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N471", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "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": "P48723-1.96.96", "start_pos": 96, "end_pos": 96, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1984160531", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1984160531", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1984160531", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1984160531#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1984160531", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1984160531", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "NDVYVGYESVELADSNPQNT", "down_seq": "YDAKRFIGKIFTAEELEAEI", "snv": [ { "evidence": [ { "id": "rs1984160531", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1984160531" }, { "id": "rs1984160531", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1984160531#frequency_tab" }, { "id": "rs1984160531", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1984160531" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTI->NTT).", "chr_id": "21", "chr_pos": "14381282", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I96", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P48723-1.98.98", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P48723-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P48723", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P48723", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VYVGYESVELADSNPQNTIY", "down_seq": "AKRFIGKIFTAEELEAEIGR", "snv": [ { "evidence": [ { "id": "P48723", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P48723" } ], "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": "21", "chr_pos": "14381277", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D98", "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: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": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P48723-1.96.96", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "P48723-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "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": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "NKLGGQDFNQRLLQYLYKQI", "down_seq": "QTYGFVPSRKEEIHRLRQAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr272" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P48723-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P48723-1.275.275", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P48723-1.280.280", "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": "P48723-1.275.275", "start_pos": 275, "end_pos": 275, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "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": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "GGQDFNQRLLQYLYKQIYQT", "down_seq": "GFVPSRKEEIHRLRQAVEMV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr275" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P48723-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P48723-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P48723-1.280.280", "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": "P48723-1.280.280", "start_pos": 280, "end_pos": 280, "uniprot_canonical_ac": "P48723-1", "length": 471, "uniprot_id": "HSP13_HUMAN", "protein_name": "Heat shock 70 kDa protein 13", "refseq_ac": "NP_008879", "refseq_name": "heat shock 70 kDa protein 13 precursor", "gene_name": "HSPA13", "gene_names_uniprotkb": "HSPA13; STCH", "gene_names_refseq": "HSPA13; STCH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P48723", "url": "https://www.uniprot.org/uniprotkb/P48723" } ], "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": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723", "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": "NQRLLQYLYKQIYQTYGFVP", "down_seq": "RKEEIHRLRQAVEMVKLNLT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P48723", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P48723" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser280" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "137", "end_pos": "137" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "200", "end_pos": "215" }, { "start_pos": "298", "end_pos": "298" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "280", "end_pos": "280" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P48723-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P48723-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P48723-1.275.275", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P48723-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P48723-1.300.300", "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": "Q12988-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "Q12988-1", "length": 150, "uniprot_id": "HSPB3_HUMAN", "protein_name": "Heat shock protein beta-3", "refseq_ac": "NP_006299", "refseq_name": "heat shock protein beta-3", "gene_name": "HSPB3", "gene_names_uniprotkb": "HSPB3; HSP27; HSPL27", "gene_names_refseq": "DHMN2C; HMN2C; HMND4; HSPB3; HSPL27", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12988", "url": "https://www.uniprot.org/uniprotkb/Q12988" } ], "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": "rs1941091560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1941091560", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1941091560", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1941091560#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EARGLEDCRLDHALYALPGP", "down_seq": "IVDLRKTRAAQSPPVDSAAE", "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": "Thr41", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1941091560", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1941091560" }, { "id": "rs1941091560", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1941091560#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": "5", "chr_pos": "54455910", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T41", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "41", "end_pos": "41" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "65", "end_pos": "65" } ] } ], "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12988-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "Q12988-1", "length": 150, "uniprot_id": "HSPB3_HUMAN", "protein_name": "Heat shock protein beta-3", "refseq_ac": "NP_006299", "refseq_name": "heat shock protein beta-3", "gene_name": "HSPB3", "gene_names_uniprotkb": "HSPB3; HSP27; HSPL27", "gene_names_refseq": "DHMN2C; HMN2C; HMND4; HSPB3; HSPL27", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12988", "url": "https://www.uniprot.org/uniprotkb/Q12988" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12988", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12988", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LPEDIIIQTFEGWLLIKAQH", "down_seq": "TRMDEHGFISRSFTRQYKLP", "snv": [ { "evidence": [ { "id": "Q12988", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12988" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "54456090", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G101", "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": "41", "end_pos": "41" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "65", "end_pos": "65" } ] } ], "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": "Q12988-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "Q12988-1", "length": 150, "uniprot_id": "HSPB3_HUMAN", "protein_name": "Heat shock protein beta-3", "refseq_ac": "NP_006299", "refseq_name": "heat shock protein beta-3", "gene_name": "HSPB3", "gene_names_uniprotkb": "HSPB3; HSP27; HSPL27", "gene_names_refseq": "DHMN2C; HMN2C; HMND4; HSPB3; HSPL27", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12988", "url": "https://www.uniprot.org/uniprotkb/Q12988" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12988", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12988", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LRKTRAAQSPPVDSAAETPP", "down_seq": "EGKSHFQILLDVVQFLPEDI", "snv": [ { "evidence": [ { "id": "Q12988", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12988" } ], "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": "5", "chr_pos": "54455983", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R65", "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": "41", "end_pos": "41" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "65", "end_pos": "65" } ] } ], "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": "Q4G112-1.329.329", "start_pos": 329, "end_pos": 329, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "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": "rs1017089", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1017089", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1017089", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1017089", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs1017089", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1017089", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs1017089", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1017089#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1017089", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1017089", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs372017544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372017544", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372017544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372017544", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372017544", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372017544#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372017544", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372017544", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AVLQCCSPTHMDALSSCVTP", "down_seq": "ASSYAHCNYFQNPSMQSSYP", "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": "Thr329", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1017089", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1017089" }, { "id": "rs1017089", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1017089" }, { "id": "rs1017089", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1017089" }, { "id": "rs1017089", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1017089#frequency_tab" }, { "id": "rs1017089", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1017089" } ], "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 (TAS->NAS); o-glyco-site-loss (T->N).", "chr_id": "17", "chr_pos": "58466919", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T329", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs372017544", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372017544" }, { "id": "rs372017544", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372017544" }, { "id": "rs372017544", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372017544#frequency_tab" }, { "id": "rs372017544", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372017544" } ], "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": "17", "chr_pos": "58466920", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T329", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1017089", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1017089" }, { "id": "rs1017089", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1017089" }, { "id": "rs1017089", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1017089" }, { "id": "rs1017089", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1017089#frequency_tab" }, { "id": "rs1017089", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1017089" } ], "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": "17", "chr_pos": "58466919", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T329", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs372017544", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372017544" }, { "id": "rs372017544", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372017544" }, { "id": "rs372017544", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372017544#frequency_tab" }, { "id": "rs372017544", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372017544" } ], "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": "17", "chr_pos": "58466920", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T329", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q4G112-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q4G112-1.342.342", "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": 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": "Q4G112-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q4G112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YGFRKVVLGGPGGGKPAGNG", "down_seq": "LHHFHNPHFRRDQPQLLVHL", "snv": [ { "evidence": [ { "id": "Q4G112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "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": "17", "chr_pos": "58487956", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P107", "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": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "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": "Q4G112-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs941202333", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs941202333", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs941202333", "url": "https://www.ensembl.org/id/rs941202333", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MEALLSTPINPNN", "down_seq": "PAKLWRLVNSPRYRSIRWDG", "snv": [ { "evidence": [ { "id": "rs941202333", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs941202333" }, { "id": "rs941202333", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs941202333" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNF->NNS).", "chr_id": "17", "chr_pos": "58488234", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F14", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q4G112-1.25.25", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q4G112-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs139274199", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139274199", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs139274199", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs139274199", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs139274199", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139274199", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs139274199", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139274199#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs139274199", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139274199", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RPEPHGPVAVGQFHRSFRRD", "down_seq": "LSPYSCVSTPSHDHSTYPLK", "snv": [ { "evidence": [ { "id": "rs139274199", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139274199" }, { "id": "rs139274199", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs139274199" }, { "id": "rs139274199", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139274199" }, { "id": "rs139274199", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139274199#frequency_tab" }, { "id": "rs139274199", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139274199" } ], "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": "17", "chr_pos": "58480222", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S199", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q4G112-1.212.212", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q4G112-1.212.212", "start_pos": 212, "end_pos": 212, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q4G112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs150369529", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150369529", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150369529", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150369529", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs150369529", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150369529", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs150369529", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150369529#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs150369529", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150369529", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HRSFRRDSLSPYSCVSTPSH", "down_seq": "HSTYPLKGLDRTPVPHRIWQ", "snv": [ { "evidence": [ { "id": "Q4G112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112" }, { "id": "rs150369529", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150369529" }, { "id": "rs150369529", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150369529" }, { "id": "rs150369529", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150369529" }, { "id": "rs150369529", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150369529#frequency_tab" }, { "id": "rs150369529", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150369529" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DHS->NHS).", "chr_id": "17", "chr_pos": "58480184", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D212", "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": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q4G112-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q4G112-1.223.223", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q4G112-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q4G112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YSCVSTPSHDHSTYPLKGLD", "down_seq": "TPVPHRIWQNSLGMHPGQVE", "snv": [ { "evidence": [ { "id": "Q4G112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "58480151", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R223", "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": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q4G112-1.212.212", "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": "Q4G112-1.25.25", "start_pos": 25, "end_pos": 25, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1312992619", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1312992619", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1312992619", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1312992619", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LSTPINPNNFPAKLWRLVNS", "down_seq": "RYRSIRWDGRGEGLLIDQPL", "snv": [ { "evidence": [ { "id": "rs1312992619", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1312992619" }, { "id": "rs1312992619", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1312992619" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSP->NSS).", "chr_id": "17", "chr_pos": "58488202", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P25", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q4G112-1.14.14", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q4G112-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q4G112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GVPFPVLQRFPTEVTYTLQP", "down_seq": "TTSVHVQQGPQTMVSSSQKY", "snv": [ { "evidence": [ { "id": "Q4G112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112" } ], "glycoeffect": [ "n-glyco-sequon-gain", "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: n-glyco-sequon-gain (STT->NTT).", "chr_id": "17", "chr_pos": "58480003", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S272", "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": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q4G112-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q4G112-1.291.291", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q4G112-1.287.287", "start_pos": 287, "end_pos": 287, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1205789349", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1205789349", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1205789349", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1205789349", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YTLQPSTTSVHVQQGPQTMV", "down_seq": "SSQKYSNYTPSAQYSQAYYP", "snv": [ { "evidence": [ { "id": "rs1205789349", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1205789349" }, { "id": "rs1205789349", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1205789349" } ], "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": "17", "chr_pos": "58479958", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S287", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q4G112-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q4G112-1.291.291", "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": "Q4G112-1.291.291", "start_pos": 291, "end_pos": 291, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1324800718", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324800718", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1324800718", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324800718", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PSTTSVHVQQGPQTMVSSSQ", "down_seq": "YSNYTPSAQYSQAYYPTAVL", "snv": [ { "evidence": [ { "id": "rs1324800718", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324800718" }, { "id": "rs1324800718", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324800718" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KYS->NYS).", "chr_id": "17", "chr_pos": "58479945", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K291", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q4G112-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q4G112-1.287.287", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q4G112-1.323.323", "start_pos": 323, "end_pos": 323, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757858300", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757858300", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757858300", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757858300", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757858300", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757858300", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QAYYPTAVLQCCSPTHMDAL", "down_seq": "SCVTPTASSYAHCNYFQNPS", "snv": [ { "evidence": [ { "id": "rs757858300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757858300" }, { "id": "rs757858300", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757858300" }, { "id": "rs757858300", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757858300" } ], "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 (SSC->NSC).", "chr_id": "17", "chr_pos": "58466937", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S323", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q4G112-1.329.329", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q4G112-1.342.342", "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": "Q4G112-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q4G112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs766204414", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766204414", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766204414", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766204414", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766204414", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766204414", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LSSCVTPTASSYAHCNYFQN", "down_seq": "SMQSSYPVEFLPSNWPCSTT", "snv": [ { "evidence": [ { "id": "Q4G112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPS->NLS).", "chr_id": "17", "chr_pos": "58463299", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P342", "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: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": "Q4G112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112" } ], "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 (NPS->NSS).", "chr_id": "17", "chr_pos": "58463300", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P342", "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": "rs766204414", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766204414" }, { "id": "rs766204414", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766204414" }, { "id": "rs766204414", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766204414" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NTS).", "chr_id": "17", "chr_pos": "58463300", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P342", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q4G112-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q4G112-1.329.329", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q4G112-1.358.358", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q4G112-1.360.360", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_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": "Q4G112-1.358.358", "start_pos": 358, "end_pos": 358, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q4G112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs547910825", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547910825", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs547910825", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs547910825", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs547910825", "url": "https://www.ncbi.nlm.nih.gov/snp/rs547910825#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YFQNPSMQSSYPVEFLPSNW", "down_seq": "CSTTDENTKTEVNLEAVFQI", "snv": [ { "evidence": [ { "id": "Q4G112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112" }, { "id": "rs547910825", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547910825" }, { "id": "rs547910825", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs547910825" }, { "id": "rs547910825", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs547910825#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NWP->NWS).", "chr_id": "17", "chr_pos": "58463252", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P358", "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", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q4G112-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q4G112-1.360.360", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q4G112-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1327083685", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1327083685", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1327083685", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1327083685#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1327083685", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1327083685", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QNPSMQSSYPVEFLPSNWPC", "down_seq": "TTDENTKTEVNLEAVFQIVD", "snv": [ { "evidence": [ { "id": "rs1327083685", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1327083685" }, { "id": "rs1327083685", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1327083685#frequency_tab" }, { "id": "rs1327083685", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1327083685" } ], "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 (STT->NTT).", "chr_id": "17", "chr_pos": "58463245", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S360", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q4G112-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q4G112-1.358.358", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q4G112-1.383.383", "start_pos": 383, "end_pos": 383, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q4G112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "DENTKTEVNLEAVFQIVDEL", "down_seq": "SSPKLEMVKVEPVENQCPTS", "snv": [ { "evidence": [ { "id": "Q4G112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HSS->NSS).", "chr_id": "17", "chr_pos": "58463177", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H383", "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": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "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": "Q4G112-1.416.416", "start_pos": 416, "end_pos": 416, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1974815241", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1974815241", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1974815241", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1974815241#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VENQCPTSPSYRGQHILANS", "down_seq": "NSNPCSASQASQLEPLTPVG", "snv": [ { "evidence": [ { "id": "rs1974815241", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1974815241" }, { "id": "rs1974815241", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1974815241#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSN->NSS).", "chr_id": "17", "chr_pos": "58463077", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N416", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q4G112-1.420.420", "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": "Q4G112-1.420.420", "start_pos": 420, "end_pos": 420, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q4G112", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs763352431", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763352431", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763352431", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763352431", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763352431", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763352431", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs901264315", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs901264315", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs901264315", "url": "https://www.ncbi.nlm.nih.gov/snp/rs901264315#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs901264315", "url": "http://gnomad.broadinstitute.org/awesome?query=rs901264315", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CPTSPSYRGQHILANSNNSN", "down_seq": "CSASQASQLEPLTPVGSDIM", "snv": [ { "evidence": [ { "id": "Q4G112", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q4G112" }, { "id": "rs763352431", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763352431" }, { "id": "rs763352431", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763352431" }, { "id": "rs763352431", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763352431" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPC->NLC).", "chr_id": "17", "chr_pos": "58463065", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P420", "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": "rs901264315", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs901264315" }, { "id": "rs901264315", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs901264315#frequency_tab" }, { "id": "rs901264315", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs901264315" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPC->NSC).", "chr_id": "17", "chr_pos": "58463066", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P420", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q4G112-1.416.416", "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": 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": "Q4G112-1.496.496", "start_pos": 496, "end_pos": 496, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs992991093", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs992991093", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs992991093", "url": "https://www.ncbi.nlm.nih.gov/snp/rs992991093#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs992991093", "url": "http://gnomad.broadinstitute.org/awesome?query=rs992991093", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QESAAIQQAHVKLKEHLNHN", "down_seq": "SPSSVVFVQEGPPFSTHQVD", "snv": [ { "evidence": [ { "id": "rs992991093", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs992991093" }, { "id": "rs992991093", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs992991093#frequency_tab" }, { "id": "rs992991093", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs992991093" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NAS).", "chr_id": "17", "chr_pos": "58462838", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P496", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs992991093", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs992991093" }, { "id": "rs992991093", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs992991093#frequency_tab" }, { "id": "rs992991093", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs992991093" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NSS).", "chr_id": "17", "chr_pos": "58462838", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P496", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q4G112-1.497.497", "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": "Q4G112-1.565.565", "start_pos": 565, "end_pos": 565, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1974748994", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1974748994", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1974748994", "url": "https://www.ensembl.org/id/rs1974748994", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASKPSEDTGLATPARYREHR", "down_seq": "NSQQGKSPDLHLLVDVACKQ", "snv": [ { "evidence": [ { "id": "rs1974748994", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1974748994" }, { "id": "rs1974748994", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1974748994" } ], "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 (SNS->NNS).", "chr_id": "17", "chr_pos": "58458794", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S565", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q4G112-1.572.572", "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": "Q4G112-1.497.497", "start_pos": 497, "end_pos": 497, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies.", "journal": "Molecular immunology", "date": "2020-07", "authors": "Pandey Kirti, Mifsud Nicole A, Lim Kam Sian Terry C C, Ayala Rochelle, Ternette Nicola, Ramarathinam Sri H, Purcell Anthony W", "evidence": [ { "database": "iPTMnet", "id": "Q4G112", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q4G112" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "Q4G112", "url": "https://www.iedb.org/epitope/Q4G112", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q4G112", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q4G112", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ESAAIQQAHVKLKEHLNHNP", "down_seq": "PSSVVFVQEGPPFSTHQVDA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q4G112", "url": "https://www.iedb.org/epitope/Q4G112" }, { "database": "iPTMnet", "id": "Q4G112", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q4G112" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ], "site_lbl": "Ser497" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q4G112-1.496.496", "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": "Q4G112-1.572.572", "start_pos": 572, "end_pos": 572, "uniprot_canonical_ac": "Q4G112-1", "length": 596, "uniprot_id": "HSF5_HUMAN", "protein_name": "Heat shock factor protein 5", "refseq_ac": "NP_001073908", "refseq_name": "heat shock factor protein 5", "gene_name": "HSF5", "gene_names_uniprotkb": "HSF5; HSTF5", "gene_names_refseq": "HSF 5; HSF5; HSTF 5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TGLATPARYREHRSNSQQGK", "down_seq": "PDLHLLVDVACKQERFPKEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q4G112", "url": "https://www.uniprot.org/uniprotkb/Q4G112" } ], "site_lbl": "Ser572" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "329", "end_pos": "329" } ] }, { "type": "snv", "site_list": [ { "start_pos": "329", "end_pos": "329" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "565", "end_pos": "565" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "497", "end_pos": "497" }, { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q4G112-1.565.565", "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": "Q58FG0-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q58FG0-1", "length": 334, "uniprot_id": "HS905_HUMAN", "protein_name": "Putative heat shock protein HSP 90-alpha A5", "refseq_ac": "", "refseq_name": "", "gene_name": "HSP90AA5P", "gene_names_uniprotkb": "HSP90AA5P; HSP90AE", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q58FG0", "url": "https://www.uniprot.org/uniprotkb/Q58FG0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q58FG0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q58FG0" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] } ], "crossref": [ { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q58FG0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q58FG0", "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": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "Q58FG0", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q58FG0" } ] } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "89", "end_pos": "89" } ] } ], "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": "Q58FG0-1.89.89", "start_pos": 89, "end_pos": 89, "uniprot_canonical_ac": "Q58FG0-1", "length": 334, "uniprot_id": "HS905_HUMAN", "protein_name": "Putative heat shock protein HSP 90-alpha A5", "refseq_ac": "", "refseq_name": "", "gene_name": "HSP90AA5P", "gene_names_uniprotkb": "HSP90AA5P; HSP90AE", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q58FG0", "url": "https://www.uniprot.org/uniprotkb/Q58FG0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q58FG0", "url": "https://www.uniprot.org/uniprotkb/Q58FG0", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EDKRKKKKESNDKPEIEDVG", "down_seq": "DEEEEKKDADKKKKKSKEKY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q58FG0", "url": "https://www.uniprot.org/uniprotkb/Q58FG0" } ], "site_lbl": "Ser89" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "89", "end_pos": "89" } ] } ], "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": "Q8NHY5-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "Q8NHY5-1", "length": 278, "uniprot_id": "HUS1B_HUMAN", "protein_name": "Checkpoint protein HUS1B", "refseq_ac": "NP_683762", "refseq_name": "checkpoint protein HUS1B", "gene_name": "HUS1B", "gene_names_uniprotkb": "HUS1B", "gene_names_refseq": "HUS1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHY5", "url": "https://www.uniprot.org/uniprotkb/Q8NHY5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHY5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHY5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SRAARSAAGASSLKLQLTHK", "down_seq": "RPSLTVAVELVSSLGRARSV", "snv": [ { "evidence": [ { "id": "Q8NHY5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHY5" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "656623", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R108", "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: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: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": "108", "end_pos": "108" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "205", "end_pos": "205" } ] } ], "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": "Q8NHY5-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "Q8NHY5-1", "length": 278, "uniprot_id": "HUS1B_HUMAN", "protein_name": "Checkpoint protein HUS1B", "refseq_ac": "NP_683762", "refseq_name": "checkpoint protein HUS1B", "gene_name": "HUS1B", "gene_names_uniprotkb": "HUS1B", "gene_names_refseq": "HUS1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHY5", "url": "https://www.uniprot.org/uniprotkb/Q8NHY5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHY5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHY5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "PSLTVAVELVSSLGRARSVV", "down_seq": "DLPVRVLPRRVWRDCLPPSL", "snv": [ { "evidence": [ { "id": "Q8NHY5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHY5" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "656555", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H130", "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": "108", "end_pos": "108" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "205", "end_pos": "205" } ] } ], "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": "Q8NHY5-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "Q8NHY5-1", "length": 278, "uniprot_id": "HUS1B_HUMAN", "protein_name": "Checkpoint protein HUS1B", "refseq_ac": "NP_683762", "refseq_name": "checkpoint protein HUS1B", "gene_name": "HUS1B", "gene_names_uniprotkb": "HUS1B", "gene_names_refseq": "HUS1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHY5", "url": "https://www.uniprot.org/uniprotkb/Q8NHY5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHY5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHY5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PRRVWRDCLPPSLRASDASI", "down_seq": "LPRWRTLRSIVERMANVGSH", "snv": [ { "evidence": [ { "id": "Q8NHY5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHY5" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "656473", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R158", "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: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" ] }, { "evidence": [ { "id": "Q8NHY5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHY5" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "656472", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R158", "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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "205", "end_pos": "205" } ] } ], "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": "Q8NHY5-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "Q8NHY5-1", "length": 278, "uniprot_id": "HUS1B_HUMAN", "protein_name": "Checkpoint protein HUS1B", "refseq_ac": "NP_683762", "refseq_name": "checkpoint protein HUS1B", "gene_name": "HUS1B", "gene_names_uniprotkb": "HUS1B", "gene_names_refseq": "HUS1B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHY5", "url": "https://www.uniprot.org/uniprotkb/Q8NHY5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHY5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHY5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LSGRMTLSIETEVVSIQSYF", "down_seq": "NLGNPPQSAVGVPENRDLES", "snv": [ { "evidence": [ { "id": "Q8NHY5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHY5" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "656331", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K205", "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" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "205", "end_pos": "205" } ] } ], "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": "O76014-1.422.422", "start_pos": 422, "end_pos": 422, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "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": "O76014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs8071814", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs8071814", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs8071814", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs8071814", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs8071814", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs8071814", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs8071814", "url": "https://www.ncbi.nlm.nih.gov/snp/rs8071814#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs8071814", "url": "http://gnomad.broadinstitute.org/awesome?query=rs8071814", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ATYRNLLESEDCKLPCNPCS", "down_seq": "PASCTSCPSCGPVTGGSPSG", "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": "Thr422", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "O76014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014" }, { "id": "rs8071814", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs8071814" }, { "id": "rs8071814", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs8071814" }, { "id": "rs8071814", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs8071814" }, { "id": "rs8071814", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs8071814#frequency_tab" }, { "id": "rs8071814", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs8071814" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "17", "chr_pos": "41420963", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T422", "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", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O76014-1.419.419", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "O76014-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Epigenetic co-regulator HCF-1 promotes lung cancer via O-GlcNAcylation-dependent pathways.", "journal": "Molecular therapy. Oncology", "date": "2025-12-18", "authors": "Srivastava Priyanka P, Dasari Abhilash, Kumar Saran, Gupta Ishaan, Jain Deepali, Minocha Shilpi", "evidence": [ { "database": "O-GlcNAc Database", "id": "O76014", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76014" } ], "reference": [ { "type": "PubMed", "id": "41018975", "url": "https://glygen.org/publication/PubMed/41018975" } ] } ], "crossref": [ { "id": "41018975", "url": "https://glygen.org/publication/PubMed/41018975", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O76014", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76014", "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": "41018975", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/41018975" }, { "id": "O76014", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76014" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "O76014-1.9.9", "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": "O76014-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs376624430", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376624430", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs376624430", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376624430", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs376624430", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376624430#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs376624430", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376624430", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AYGKNTLNGHEKETMKFLND", "down_seq": "LANYLEKVRQLEQENAELET", "snv": [ { "evidence": [ { "id": "rs376624430", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376624430" }, { "id": "rs376624430", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376624430" }, { "id": "rs376624430", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376624430#frequency_tab" }, { "id": "rs376624430", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376624430" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDR->NDC).", "chr_id": "17", "chr_pos": "41424184", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R114", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "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": "O76014-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EQENAELETTLLERSKCHES", "down_seq": "VCPDYQSYFRTIEELQQKIL", "snv": [ { "evidence": [ { "id": "O76014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TVC->NVC).", "chr_id": "17", "chr_pos": "41424087", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T146", "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": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "O76014-1.151.151", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "O76014-1.151.151", "start_pos": 151, "end_pos": 151, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1009033591", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1009033591", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1009033591", "url": "https://www.ensembl.org/id/rs1009033591", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ELETTLLERSKCHESTVCPD", "down_seq": "QSYFRTIEELQQKILCSKAE", "snv": [ { "evidence": [ { "id": "rs1009033591", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1009033591" }, { "id": "rs1009033591", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1009033591" } ], "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": "17", "chr_pos": "41424073", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y151", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "O76014-1.146.146", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76014-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ADDFRIKLESERSLHQLVEA", "down_seq": "KCGTQKLLDDATLAKADLEA", "snv": [ { "evidence": [ { "id": "O76014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DKC->NKC).", "chr_id": "17", "chr_pos": "41422894", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D206", "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": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "O76014-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O76014-1.217.217", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "O76014-1.216.216", "start_pos": 216, "end_pos": 216, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1407474978", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1407474978", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1407474978", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1407474978", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ERSLHQLVEADKCGTQKLLD", "down_seq": "ATLAKADLEAQQESLKEEQL", "snv": [ { "evidence": [ { "id": "rs1407474978", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1407474978" }, { "id": "rs1407474978", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1407474978" } ], "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": "17", "chr_pos": "41422864", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D216", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O76014-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O76014-1.217.217", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76014-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RSLHQLVEADKCGTQKLLDD", "down_seq": "TLAKADLEAQQESLKEEQLS", "snv": [ { "evidence": [ { "id": "O76014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "41422861", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A217", "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: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": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O76014-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O76014-1.216.216", "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": "O76014-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770877466", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770877466", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770877466", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770877466", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770877466", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770877466#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs770877466", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770877466", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "FYSTSSCPLGCTMAPGARNV", "down_seq": "VSPIDVGCQPVAEANAASMC", "snv": [ { "evidence": [ { "id": "rs770877466", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770877466" }, { "id": "rs770877466", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770877466" }, { "id": "rs770877466", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770877466#frequency_tab" }, { "id": "rs770877466", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770877466" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVF->NVS).", "chr_id": "17", "chr_pos": "41424453", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F24", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O76014-1.9.9", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76014-1.341.341", "start_pos": 341, "end_pos": 341, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LELRCTVNALEVERQAQHTL", "down_seq": "DCLQNSLCEAEDRYGTELAQ", "snv": [ { "evidence": [ { "id": "O76014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014" } ], "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 (KDC->NDC).", "chr_id": "17", "chr_pos": "41421585", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K341", "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": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "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": "O76014-1.419.419", "start_pos": 419, "end_pos": 419, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1175765157", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1175765157", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1175765157", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1175765157#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1175765157", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1175765157", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs775896953", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775896953", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775896953", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775896953", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775896953", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775896953", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NEIATYRNLLESEDCKLPCN", "down_seq": "CSTPASCTSCPSCGPVTGGS", "snv": [ { "evidence": [ { "id": "O76014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014" }, { "id": "rs1175765157", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1175765157" }, { "id": "rs1175765157", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1175765157#frequency_tab" }, { "id": "rs1175765157", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1175765157" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPC->NLC).", "chr_id": "17", "chr_pos": "41420972", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P419", "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": "rs775896953", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775896953" }, { "id": "rs775896953", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775896953" }, { "id": "rs775896953", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775896953" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPC->NSC).", "chr_id": "17", "chr_pos": "41420973", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P419", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775896953", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775896953" }, { "id": "rs775896953", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775896953" }, { "id": "rs775896953", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775896953" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPC->NTC).", "chr_id": "17", "chr_pos": "41420973", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P419", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "O76014-1.422.422", "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": 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": "O76014-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1339539969", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1339539969", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1339539969", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1339539969#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1339539969", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1339539969", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VGCQPVAEANAASMCLLANV", "down_seq": "HANRVRVGSTPLGRPSLCLP", "snv": [ { "evidence": [ { "id": "rs1339539969", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1339539969" }, { "id": "rs1339539969", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1339539969#frequency_tab" }, { "id": "rs1339539969", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1339539969" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVA->NVT).", "chr_id": "17", "chr_pos": "41424376", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A50", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "O76014-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O76014-1.66.66", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76014-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CLLANVAHANRVRVGSTPLG", "down_seq": "PSLCLPPTSHTACPLPGTCH", "snv": [ { "evidence": [ { "id": "O76014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "41424334", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R64", "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": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O76014-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O76014-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O76014-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O76014-1.75.75", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "O76014-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1273496695", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1273496695", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1273496695", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1273496695#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1273496695", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1273496695", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LANVAHANRVRVGSTPLGRP", "down_seq": "LCLPPTSHTACPLPGTCHIP", "snv": [ { "evidence": [ { "id": "rs1273496695", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1273496695" }, { "id": "rs1273496695", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1273496695#frequency_tab" }, { "id": "rs1273496695", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1273496695" } ], "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 (SLC->NLC).", "chr_id": "17", "chr_pos": "41424327", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S66", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O76014-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O76014-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O76014-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O76014-1.75.75", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76014-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1174567937", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1174567937", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1174567937", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1174567937#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1174567937", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1174567937", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NRVRVGSTPLGRPSLCLPPT", "down_seq": "HTACPLPGTCHIPGNIGICG", "snv": [ { "evidence": [ { "id": "rs1174567937", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1174567937" }, { "id": "rs1174567937", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1174567937#frequency_tab" }, { "id": "rs1174567937", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1174567937" } ], "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 (SHT->NHT).", "chr_id": "17", "chr_pos": "41424306", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S73", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O76014-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O76014-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O76014-1.75.75", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76014-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2018584600", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2018584600", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2018584600", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2018584600#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VRVGSTPLGRPSLCLPPTSH", "down_seq": "ACPLPGTCHIPGNIGICGAY", "snv": [ { "evidence": [ { "id": "rs2018584600", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2018584600" }, { "id": "rs2018584600", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2018584600#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 (TAC->NAC).", "chr_id": "17", "chr_pos": "41424300", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T75", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O76014-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O76014-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O76014-1.73.73", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76014-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "O76014-1", "length": 449, "uniprot_id": "KRT37_HUMAN", "protein_name": "Keratin, type I cuticular Ha7", "refseq_ac": "NP_003761", "refseq_name": "keratin, type I cuticular Ha7", "gene_name": "KRT37", "gene_names_uniprotkb": "KRT37; HHA7; HKA7; KRTHA7", "gene_names_refseq": "HA7; K37; KRT37; KRTHA7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76014", "url": "https://www.uniprot.org/uniprotkb/O76014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MTSFYSTS", "down_seq": "CPLGCTMAPGARNVFVSPID", "snv": [ { "evidence": [ { "id": "O76014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76014" } ], "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: num. of cancers (3).", "chr_id": "17", "chr_pos": "41424498", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S9", "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: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": "422", "end_pos": "422" } ] }, { "type": "snv", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O76014-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O76014-1.24.24", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q15024-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "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": "KLEKPNEGYLEFFVDCSASA", "down_seq": "PEFEGRGGDDLGTEIANTLY", "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": "Thr90", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q15024-1.77.77", "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": "Q15024-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "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": "Q15024", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q15024" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q15024", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q15024" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "Q15024", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q15024" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q15024", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q15024", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "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": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q15024", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q15024" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q15024-1.5.5", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q15024-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15024", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15024", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PEFEGRGGDDLGTEIANTLY", "down_seq": "IFNNKSSVDLKTLCISPREH", "snv": [ { "evidence": [ { "id": "Q15024", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15024" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "44997163", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R111", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q15024-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q15024-1.129.129", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q15024-1.123.123", "start_pos": 123, "end_pos": 123, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1706745968", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1706745968", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1706745968", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1706745968#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TEIANTLYRIFNNKSSVDLK", "down_seq": "LCISPREHCWVLYVDVLLLE", "snv": [ { "evidence": [ { "id": "rs1706745968", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1706745968" }, { "id": "rs1706745968", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1706745968#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 (TLC->NLC).", "chr_id": "3", "chr_pos": "44997200", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T123", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q15024-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q15024-1.129.129", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15024-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15024", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15024", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LYRIFNNKSSVDLKTLCISP", "down_seq": "EHCWVLYVDVLLLECGGNLF", "snv": [ { "evidence": [ { "id": "Q15024", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15024" } ], "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 (4).", "chr_id": "3", "chr_pos": "44997218", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R129", "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: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": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q15024-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q15024-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q15024-1.149.149", "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": "Q15024-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1284304750", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1284304750", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1284304750", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1284304750", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "REHCWVLYVDVLLLECGGNL", "down_seq": "DAISIAVKAALFNTRIPRVR", "snv": [ { "evidence": [ { "id": "rs1284304750", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1284304750" }, { "id": "rs1284304750", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1284304750" } ], "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": "45001563", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F149", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q15024-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q15024-1.164.164", "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": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15024-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762638022", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762638022", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762638022", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762638022", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762638022", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762638022#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762638022", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762638022", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CGGNLFDAISIAVKAALFNT", "down_seq": "IPRVRVLEDEEGSKDIELSD", "snv": [ { "evidence": [ { "id": "rs762638022", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762638022" }, { "id": "rs762638022", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762638022" }, { "id": "rs762638022", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762638022#frequency_tab" }, { "id": "rs762638022", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762638022" } ], "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": "3", "chr_pos": "45005291", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R164", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q15024-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q15024-1.177.177", "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": "Q15024-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15024", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15024", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KDIELSDDPYDCIRLSVENV", "down_seq": "CIVTLCKIGYRHVVDATLQE", "snv": [ { "evidence": [ { "id": "Q15024", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15024" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NVP->NVS).", "chr_id": "3", "chr_pos": "45005391", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P198", "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": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q15024-1.200.200", "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": "Q15024-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1009377956", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1009377956", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1009377956", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1009377956#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1009377956", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1009377956", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "IELSDDPYDCIRLSVENVPC", "down_seq": "VTLCKIGYRHVVDATLQEEA", "snv": [ { "evidence": [ { "id": "rs1009377956", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1009377956" }, { "id": "rs1009377956", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1009377956#frequency_tab" }, { "id": "rs1009377956", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1009377956" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IVT->NVT).", "chr_id": "3", "chr_pos": "45005398", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I200", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q15024-1.198.198", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15024-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15024", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15024", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "EMMETGKRVGKVLHASLQSV", "down_seq": "HKEESLGPKRQKVGFLG", "snv": [ { "evidence": [ { "id": "Q15024", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15024" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "V", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "3", "chr_pos": "45011283", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "V274", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q15024-1.258.258", "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": 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": "Q15024-1.46.46", "start_pos": 46, "end_pos": 46, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1474682785", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1474682785", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1474682785", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1474682785", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GRGCEDYRCVEVETDVVSNT", "down_seq": "GSARVKLGHTDILVGVKAEM", "snv": [ { "evidence": [ { "id": "rs1474682785", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1474682785" }, { "id": "rs1474682785", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1474682785" } ], "glycoeffect": [ "n-glyco-sequon-gain", "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SGS->NGS).", "chr_id": "3", "chr_pos": "44989219", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S46", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "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": "Q15024-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15024", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15024", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ARVKLGHTDILVGVKAEMGT", "down_seq": "KLEKPNEGYLEFFVDCSASA", "snv": [ { "evidence": [ { "id": "Q15024", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15024" } ], "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 (3).", "chr_id": "3", "chr_pos": "44989596", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P69", "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: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": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q15024-1.77.77", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q15024-1.77.77", "start_pos": 77, "end_pos": 77, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1489697550", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1489697550", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1489697550", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1489697550", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DILVGVKAEMGTPKLEKPNE", "down_seq": "YLEFFVDCSASATPEFEGRG", "snv": [ { "evidence": [ { "id": "rs1489697550", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1489697550" }, { "id": "rs1489697550", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1489697550" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEG->NES).", "chr_id": "3", "chr_pos": "44989619", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G77", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q15024-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q15024-1.90.90", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q15024-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "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": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" }, { "database": "iPTMnet", "id": "Q15024", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15024" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q15024", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15024" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q15024", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15024", "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": "KAALFNTRIPRVRVLEDEEG", "down_seq": "KDIELSDDPYDCIRLSVENV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q15024", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15024" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser177" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q15024-1.164.164", "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": "Q15024-1.258.258", "start_pos": 258, "end_pos": 258, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "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": "Q15024", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15024" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q15024", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15024", "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": "CMRKVGKGSLDPESIFEMME", "down_seq": "GKRVGKVLHASLQSVVHKEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q15024", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15024" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr258" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q15024-1.274.274", "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": "Q15024-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "Q15024-1", "length": 291, "uniprot_id": "EXOS7_HUMAN", "protein_name": "Exosome complex component RRP42", "refseq_ac": "NP_055819", "refseq_name": "exosome complex component RRP42", "gene_name": "EXOSC7", "gene_names_uniprotkb": "EXOSC7; KIAA0116; RRP42", "gene_names_refseq": "EAP1; EXOSC7; RRP42; Rrp42p; hRrp42p; p8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15024", "url": "https://www.uniprot.org/uniprotkb/Q15024" } ], "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": "Q15024", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15024" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q15024", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15024", "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": "MASV", "down_seq": "LSEAEKVYIVHGVQEDLRVD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q15024", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15024" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr5" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q15024-1.0.0", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9UL51-1.17.17", "start_pos": 17, "end_pos": 17, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "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": "rs1444877577", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1444877577", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1444877577", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1444877577", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs918660090", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs918660090", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs918660090", "url": "https://www.ensembl.org/id/rs918660090", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MDARGGGGRPGESPGA", "down_seq": "PAPGPPPPPPPAPPQQQPPP", "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": "Thr17", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1444877577", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1444877577" }, { "id": "rs1444877577", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1444877577" } ], "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": "19", "chr_pos": "589995", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T17", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs918660090", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs918660090" }, { "id": "rs918660090", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs918660090" } ], "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": "19", "chr_pos": "589994", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T17", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "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" ] }, { "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": "Q9UL51-1.407.407", "start_pos": 407, "end_pos": 407, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LVPMLQDFPRNCWVSINGMV", "down_seq": "HSWSELYSFALFKAMSHMLC", "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": "Asn407", "evidence": [ { "id": "Q9UL51", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9UL51#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9UL51-1.399.399", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UL51-1.409.409", "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": "Q9UL51-1.792.792", "start_pos": 792, "end_pos": 792, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9UL51", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9UL51" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "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": "Q9UL51", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9UL51" }, { "database": "O-GlcNAc Atlas", "id": "Q9UL51", "url": "https://oglcnac.org/atlas/detail/Q9UL51" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "iPTMnet", "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9UL51", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9UL51", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9UL51", "url": "https://oglcnac.org/atlas/detail/Q9UL51", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1295812381", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1295812381", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1295812381", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1295812381", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1341931180", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1341931180", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1341931180", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1341931180#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1341931180", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1341931180", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PGPPPPASPPGAPASPRAPR", "down_seq": "SPYGGLPAAPLAGPALPARR", "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": "Thr792", "evidence": [ { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "Q9UL51", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9UL51" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "Q9UL51", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q9UL51" } ] } ], "snv": [ { "evidence": [ { "id": "rs1295812381", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1295812381" }, { "id": "rs1295812381", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1295812381" } ], "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": "19", "chr_pos": "616178", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T792", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1341931180", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1341931180" }, { "id": "rs1341931180", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1341931180#frequency_tab" }, { "id": "rs1341931180", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1341931180" } ], "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": "19", "chr_pos": "616179", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T792", "disease": [ { "disease_id": "DOID:0111310", "recommended_name": { "id": "DOID:0111310", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111310", "name": "familial febrile seizures 2", "description": "A familial febrile seizures that has_material_basis_in variation in a region on chromosome 19p13.3." }, "synonyms": [ { "id": "DOID:0111310", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111310", "name": "FEB2", "description": "" }, { "id": "DOID:0111310", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111310", "name": "familial febrile convulsions 2", "description": "" }, { "id": "MONDO:0100519", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100519", "name": "epilepsy, idiopathic generalized, susceptibility to, 17", "description": "" }, { "id": "MONDO:0100519", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100519", "name": "EIG17", "description": "" }, { "id": "MIM:602477", "resource": "MIM", "url": "https://www.omim.org/entry/602477", "name": "Epilepsy, idiopathic generalized 17", "description": "Epilepsy, idiopathic generalized 17" } ], "unlinked_id_list": [], "evidence": [ { "id": "602477", "database": "MIM", "url": "https://www.omim.org/entry/602477" }, { "id": "0111310", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111310" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Thr792" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9UL51-1.779.779", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9UL51-1.786.786", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9UL51-1.795.795", "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": 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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9UL51-1.851.851", "start_pos": 851, "end_pos": 851, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "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": "rs992075582", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs992075582", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs992075582", "url": "https://www.ncbi.nlm.nih.gov/snp/rs992075582#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs992075582", "url": "http://gnomad.broadinstitute.org/awesome?query=rs992075582", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs917842519", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs917842519", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs917842519", "url": "https://www.ncbi.nlm.nih.gov/snp/rs917842519#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs917842519", "url": "http://gnomad.broadinstitute.org/awesome?query=rs917842519", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "APGPAASTRPASSSTPRLGP", "down_seq": "PAARAAAPSPDRRDSASPGA", "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": "Thr851", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs992075582", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs992075582" }, { "id": "rs992075582", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs992075582#frequency_tab" }, { "id": "rs992075582", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs992075582" } ], "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": "19", "chr_pos": "616355", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T851", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs917842519", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs917842519" }, { "id": "rs917842519", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs917842519#frequency_tab" }, { "id": "rs917842519", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs917842519" } ], "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": "19", "chr_pos": "616356", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T851", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q9UL51-1.866.866", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9UL51-1.868.868", "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": "Q9UL51-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "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": "rs1600512594", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600512594", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600512594", "url": "https://www.ensembl.org/id/rs1600512594", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2512439491", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2512439491", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DEGGPRGRLRSRDSSCGRPG", "down_seq": "PGAASTAKGSPNGECGRGEP", "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": "Thr87", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1600512594", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600512594" }, { "id": "rs1600512594", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600512594" } ], "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": "19", "chr_pos": "590205", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T87", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2512439491", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2512439491" } ], "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": "19", "chr_pos": "590204", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T87", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9UL51-1.79.79", "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": 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": "Q9UL51-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1173969754", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1173969754", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1173969754", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1173969754#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WIVFNVVSDTFFLMDLVLNF", "down_seq": "TGIVIEDNTEIILDPEKIKK", "snv": [ { "evidence": [ { "id": "rs1173969754", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1173969754" }, { "id": "rs1173969754", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1173969754#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFR->NFC).", "chr_id": "19", "chr_pos": "603701", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R264", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q9UL51-1.271.271", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UL51-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs766829743", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766829743", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766829743", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766829743", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766829743", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766829743", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SDTFFLMDLVLNFRTGIVIE", "down_seq": "NTEIILDPEKIKKKYLRTWF", "snv": [ { "evidence": [ { "id": "rs766829743", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766829743" }, { "id": "rs766829743", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766829743" }, { "id": "rs766829743", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766829743" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DNT->NNT).", "chr_id": "19", "chr_pos": "603722", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D271", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9UL51-1.264.264", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UL51-1.371.371", "start_pos": 371, "end_pos": 371, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EEIFHMTYDLASAVMRICNL", "down_seq": "SMMLLLCHWDGCLQFLVPML", "snv": [ { "evidence": [ { "id": "Q9UL51", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLI->NLT).", "chr_id": "19", "chr_pos": "605116", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "I371", "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": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "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": "Q9UL51-1.399.399", "start_pos": 399, "end_pos": 399, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1185094567", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1185094567", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1185094567", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1185094567", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "HWDGCLQFLVPMLQDFPRNC", "down_seq": "VSINGMVNHSWSELYSFALF", "snv": [ { "evidence": [ { "id": "rs1185094567", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1185094567" }, { "id": "rs1185094567", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1185094567" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "W", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCW->NCC).", "chr_id": "19", "chr_pos": "605201", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W399", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q9UL51-1.407.407", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9UL51-1.409.409", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UL51-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756318406", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756318406", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756318406", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756318406", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756318406", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756318406", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs746045391", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746045391", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746045391", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746045391", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746045391", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746045391", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9UL51", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PMLQDFPRNCWVSINGMVNH", "down_seq": "WSELYSFALFKAMSHMLCIG", "snv": [ { "evidence": [ { "id": "rs756318406", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756318406" }, { "id": "rs756318406", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756318406" }, { "id": "rs756318406", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756318406" } ], "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 (NHS->NHL).", "chr_id": "19", "chr_pos": "607971", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S409", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746045391", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746045391" }, { "id": "rs746045391", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746045391" }, { "id": "rs746045391", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746045391" } ], "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 (NHS->NHP).", "chr_id": "19", "chr_pos": "607970", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S409", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9UL51", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NHS->NHW).", "chr_id": "19", "chr_pos": "607971", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S409", "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": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9UL51-1.399.399", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UL51-1.407.407", "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": 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": "Q9UL51-1.437.437", "start_pos": 437, "end_pos": 437, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1600530101", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600530101", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600530101", "url": "https://www.ensembl.org/id/rs1600530101", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALFKAMSHMLCIGYGRQAPE", "down_seq": "MTDIWLTMLSMIVGATCYAM", "snv": [ { "evidence": [ { "id": "rs1600530101", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600530101" }, { "id": "rs1600530101", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600530101" } ], "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 (SMT->NMT).", "chr_id": "19", "chr_pos": "608055", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S437", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "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": "Q9UL51-1.525.525", "start_pos": 525, "end_pos": 525, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs900889696", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs900889696", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs900889696", "url": "https://www.ensembl.org/id/rs900889696", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "EHRYQGKMFDEDSILGELNG", "down_seq": "LREEIVNFNCRKLVASMPLF", "snv": [ { "evidence": [ { "id": "rs900889696", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs900889696" }, { "id": "rs900889696", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs900889696" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGP->NGS).", "chr_id": "19", "chr_pos": "610394", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P525", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q9UL51-1.534.534", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UL51-1.534.534", "start_pos": 534, "end_pos": 534, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776729513", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776729513", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776729513", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776729513", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776729513", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776729513", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DEDSILGELNGPLREEIVNF", "down_seq": "CRKLVASMPLFANADPNFVT", "snv": [ { "evidence": [ { "id": "rs776729513", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776729513" }, { "id": "rs776729513", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776729513" }, { "id": "rs776729513", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776729513" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFN->NFS).", "chr_id": "19", "chr_pos": "613264", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N534", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q9UL51-1.525.525", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UL51-1.574.574", "start_pos": 574, "end_pos": 574, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "TAMLTKLKFEVFQPGDYIIR", "down_seq": "GTIGKKMYFIQHGVVSVLTK", "snv": [ { "evidence": [ { "id": "Q9UL51", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "613383", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E574", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "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": "Q9UL51-1.603.603", "start_pos": 603, "end_pos": 603, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "FIQHGVVSVLTKGNKEMKLS", "down_seq": "GSYFGEICLLTRGRRTASVR", "snv": [ { "evidence": [ { "id": "Q9UL51", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51" } ], "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 (DGS->NGS).", "chr_id": "19", "chr_pos": "613470", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D603", "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": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9UL51-1.608.608", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9UL51-1.608.608", "start_pos": 608, "end_pos": 608, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VVSVLTKGNKEMKLSDGSYF", "down_seq": "EICLLTRGRRTASVRADTYC", "snv": [ { "evidence": [ { "id": "Q9UL51", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "613485", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G608", "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": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9UL51-1.603.603", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9UL51-1.632.632", "start_pos": 632, "end_pos": 632, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLTRGRRTASVRADTYCRLY", "down_seq": "LSVDNFNEVLEEYPMMRRAF", "snv": [ { "evidence": [ { "id": "Q9UL51", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "613921", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S632", "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: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": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q9UL51-1.639.639", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9UL51-1.649.649", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9UL51-1.639.639", "start_pos": 639, "end_pos": 639, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs148730222", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148730222", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs148730222", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148730222", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs148730222", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148730222", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TASVRADTYCRLYSLSVDNF", "down_seq": "EVLEEYPMMRRAFETVAIDR", "snv": [ { "evidence": [ { "id": "rs148730222", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148730222" }, { "id": "rs148730222", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148730222" }, { "id": "rs148730222", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148730222" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFN->NFS).", "chr_id": "19", "chr_pos": "613942", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N639", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs148730222", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148730222" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFN->NFT).", "chr_id": "19", "chr_pos": "613942", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N639", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9UL51-1.632.632", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9UL51-1.649.649", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q9UL51-1.649.649", "start_pos": 649, "end_pos": 649, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RLYSLSVDNFNEVLEEYPMM", "down_seq": "RAFETVAIDRLDRIGKKNSI", "snv": [ { "evidence": [ { "id": "Q9UL51", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UL51" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "613971", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R649", "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": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9UL51-1.632.632", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9UL51-1.639.639", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9UL51-1.666.666", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9UL51-1.668.668", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9UL51-1.669.669", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9UL51-1.666.666", "start_pos": 666, "end_pos": 666, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757331938", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757331938", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757331938", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757331938", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757331938", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757331938#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757331938", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757331938", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PMMRRAFETVAIDRLDRIGK", "down_seq": "NSILLHKVQHDLNSGVFNNQ", "snv": [ { "evidence": [ { "id": "rs757331938", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757331938" }, { "id": "rs757331938", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757331938" }, { "id": "rs757331938", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757331938#frequency_tab" }, { "id": "rs757331938", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757331938" } ], "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": "19", "chr_pos": "615802", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K666", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9UL51-1.649.649", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UL51-1.668.668", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9UL51-1.669.669", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UL51-1.669.669", "start_pos": 669, "end_pos": 669, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs745972616", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745972616", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745972616", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745972616", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745972616", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745972616#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs745972616", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745972616", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "RRAFETVAIDRLDRIGKKNS", "down_seq": "LLHKVQHDLNSGVFNNQENA", "snv": [ { "evidence": [ { "id": "rs745972616", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745972616" }, { "id": "rs745972616", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745972616" }, { "id": "rs745972616", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745972616#frequency_tab" }, { "id": "rs745972616", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745972616" } ], "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": "19", "chr_pos": "615810", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I669", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9UL51-1.649.649", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9UL51-1.666.666", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9UL51-1.668.668", "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": "Q9UL51-1.690.690", "start_pos": 690, "end_pos": 690, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1983883302", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1983883302", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1983883302", "url": "https://www.ensembl.org/id/rs1983883302", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LLHKVQHDLNSGVFNNQENA", "down_seq": "IQEIVKYDREMVQQAELGQR", "snv": [ { "evidence": [ { "id": "rs1983883302", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1983883302" }, { "id": "rs1983883302", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1983883302" } ], "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": "19", "chr_pos": "615873", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I690", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "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": "Q9UL51-1.727.727", "start_pos": 727, "end_pos": 727, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780998820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780998820", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780998820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780998820", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780998820", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780998820", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LGQRVGLFPPPPPPPQVTSA", "down_seq": "ATLQQAAAMSFCPQVARPLV", "snv": [ { "evidence": [ { "id": "rs780998820", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780998820" }, { "id": "rs780998820", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780998820" }, { "id": "rs780998820", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780998820" } ], "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": "19", "chr_pos": "615984", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I727", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "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": "Q9UL51-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2144499114", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2144499114", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2144499114", "url": "https://www.ensembl.org/id/rs2144499114", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EALPPEAADEGGPRGRLRSR", "down_seq": "SSCGRPGTPGAASTAKGSPN", "snv": [ { "evidence": [ { "id": "rs2144499114", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2144499114" }, { "id": "rs2144499114", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2144499114" } ], "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": "19", "chr_pos": "590180", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D79", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q9UL51-1.87.87", "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": "Q9UL51-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SCRGAASGPAPGPGPAEEAG", "down_seq": "EEAGPAGEPRGSQASFMQRQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "site_lbl": "Ser146" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q9UL51-1.161.161", "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": "Q9UL51-1.161.161", "start_pos": 161, "end_pos": 161, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AEEAGSEEAGPAGEPRGSQA", "down_seq": "FMQRQFGALLQPGVNKFSLR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "site_lbl": "Ser161" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9UL51-1.146.146", "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": "Q9UL51-1.476.476", "start_pos": 476, "end_pos": 476, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A novel mechanism of modulation of hyperpolarization-activated cyclic nucleotide-gated channels by Src kinase.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Zong X, Eckert C, Yuan H, Wahl-Schott C, Abicht H, Fang L, Li R, Mistrik P, Gerstner A, Much B, Baumann L, Michalakis S, Zeng R, Chen Z, Biel M", "evidence": [ { "database": "iPTMnet", "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51" } ], "reference": [ { "type": "PubMed", "id": "16079136", "url": "https://glygen.org/publication/PubMed/16079136" } ] }, { "title": "Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6.", "journal": "Nature structural & molecular biology", "date": "2015", "authors": "Park E, Kim N, Ficarro SB, Zhang Y, Lee BI, Cho A, Kim K, Park AKJ, Park WY, Murray B, Meyerson M, Beroukhim R, Marto JA, Cho J, Eck MJ", "evidence": [ { "database": "iPTMnet", "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51" } ], "reference": [ { "type": "PubMed", "id": "26280531", "url": "https://glygen.org/publication/PubMed/26280531" } ] } ], "crossref": [ { "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16079136", "url": "https://glygen.org/publication/PubMed/16079136", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26280531", "url": "https://glygen.org/publication/PubMed/26280531", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "AMFIGHATALIQSLDSSRRQ", "down_seq": "QEKYKQVEQYMSFHKLPADF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51" }, { "database": "PubMed", "id": "16079136", "url": "https://glygen.org/publication/PubMed/16079136" }, { "database": "PubMed", "id": "26280531", "url": "https://glygen.org/publication/PubMed/26280531" } ], "site_lbl": "Tyr476" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9UL51-1.668.668", "start_pos": 668, "end_pos": 668, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The cGMP-dependent protein kinase II Is an inhibitory modulator of the hyperpolarization-activated HCN2 channel.", "journal": "PloS one", "date": "2011", "authors": "Hammelmann V, Zong X, Hofmann F, Michalakis S, Biel M", "evidence": [ { "database": "iPTMnet", "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51" } ], "reference": [ { "type": "PubMed", "id": "21347269", "url": "https://glygen.org/publication/PubMed/21347269" } ] } ], "crossref": [ { "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21347269", "url": "https://glygen.org/publication/PubMed/21347269", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MRRAFETVAIDRLDRIGKKN", "down_seq": "ILLHKVQHDLNSGVFNNQEN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q13237-1", "kinase_gene_name": "PRKG2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51" }, { "database": "PubMed", "id": "21347269", "url": "https://glygen.org/publication/PubMed/21347269" } ], "site_lbl": "Ser668" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by PKG/PRKG2", "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "site_lbl": "Ser668" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9UL51-1.649.649", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UL51-1.666.666", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9UL51-1.669.669", "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": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9UL51-1.754.754", "start_pos": 754, "end_pos": 754, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AAMSFCPQVARPLVGPLALG", "down_seq": "PRLVRRPPPGPAPAAASPGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "site_lbl": "Ser754" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q9UL51-1.771.771", "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": "Q9UL51-1.771.771", "start_pos": 771, "end_pos": 771, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALGSPRLVRRPPPGPAPAAA", "down_seq": "PGPPPPASPPGAPASPRAPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "site_lbl": "Ser771" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9UL51-1.754.754", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9UL51-1.779.779", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9UL51-1.786.786", "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": "Q9UL51-1.779.779", "start_pos": 779, "end_pos": 779, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RRPPPGPAPAAASPGPPPPA", "down_seq": "PPGAPASPRAPRTSPYGGLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "site_lbl": "Ser779" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9UL51-1.771.771", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9UL51-1.786.786", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9UL51-1.792.792", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9UL51-1.795.795", "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": "Q9UL51-1.786.786", "start_pos": 786, "end_pos": 786, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APAAASPGPPPPASPPGAPA", "down_seq": "PRAPRTSPYGGLPAAPLAGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "site_lbl": "Ser786" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9UL51-1.771.771", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9UL51-1.779.779", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9UL51-1.792.792", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9UL51-1.795.795", "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": "Q9UL51-1.795.795", "start_pos": 795, "end_pos": 795, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "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": "iPTMnet", "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PPPASPPGAPASPRAPRTSP", "down_seq": "GGLPAAPLAGPALPARRLSR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9UL51", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9UL51" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Tyr795" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9UL51-1.779.779", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9UL51-1.786.786", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9UL51-1.792.792", "categories": [ "glycosylation_flag", "snv_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": "Q9UL51-1.866.866", "start_pos": 866, "end_pos": 866, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PRLGPTPAARAAAPSPDRRD", "down_seq": "ASPGAAGGLDPQDSARSRLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "site_lbl": "Ser866" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9UL51-1.851.851", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9UL51-1.868.868", "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": "Q9UL51-1.868.868", "start_pos": 868, "end_pos": 868, "uniprot_canonical_ac": "Q9UL51-1", "length": 889, "uniprot_id": "HCN2_HUMAN", "protein_name": "Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "refseq_ac": "NP_001185", "refseq_name": "potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2", "gene_name": "HCN2", "gene_names_uniprotkb": "HCN2; BCNG2", "gene_names_refseq": "BCNG-2; BCNG2; EIG17; FEB2; GEFSP11; HAC-1; HCN2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGPTPAARAAAPSPDRRDSA", "down_seq": "PGAAGGLDPQDSARSRLSSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9UL51", "url": "https://www.uniprot.org/uniprotkb/Q9UL51" } ], "site_lbl": "Ser868" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "snv", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "669", "end_pos": "669" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "851", "end_pos": "851" }, { "start_pos": "87", "end_pos": "87" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "868", "end_pos": "868" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9UL51-1.851.851", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9UL51-1.866.866", "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": "Q8WYK2-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "Q8WYK2-1", "length": 163, "uniprot_id": "JDP2_HUMAN", "protein_name": "Jun dimerization protein 2", "refseq_ac": "NP_001128519", "refseq_name": "jun dimerization protein 2 isoform a", "gene_name": "JDP2", "gene_names_uniprotkb": "JDP2", "gene_names_refseq": "JDP2; JUNDM2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYK2", "url": "https://www.uniprot.org/uniprotkb/Q8WYK2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Genotoxic stress-triggered beta-catenin/JDP2/PRMT5 complex facilitates reestablishing glutathione homeostasis.", "journal": "Nature communications", "date": "2019", "authors": "Cao L, Wu G, Zhu J, Tan Z, Shi D, Wu X, Tang M, Li Z, Hu Y, Zhang S, Yu R, Mo S, Wu J, Song E, Li M, Song L, Li J", "evidence": [ { "database": "iPTMnet", "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2" } ], "reference": [ { "type": "PubMed", "id": "31434880", "url": "https://glygen.org/publication/PubMed/31434880" } ] } ], "crossref": [ { "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "31434880", "url": "https://glygen.org/publication/PubMed/31434880", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RTEFLQRESERLELMNAELK", "down_seq": "QIEELKQERQQLILMLNRHR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2" }, { "database": "PubMed", "id": "31434880", "url": "https://glygen.org/publication/PubMed/31434880" } ], "site_lbl": "Thr116" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "148", "end_pos": "148" } ] } ], "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": "Q8WYK2-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "Q8WYK2-1", "length": 163, "uniprot_id": "JDP2_HUMAN", "protein_name": "Jun dimerization protein 2", "refseq_ac": "NP_001128519", "refseq_name": "jun dimerization protein 2 isoform a", "gene_name": "JDP2", "gene_names_uniprotkb": "JDP2", "gene_names_refseq": "JDP2; JUNDM2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYK2", "url": "https://www.uniprot.org/uniprotkb/Q8WYK2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The AP-1 repressor, JDP2, is a bona fide substrate for the c-Jun N-terminal kinase.", "journal": "FEBS letters", "date": "2001", "authors": "Katz S, Heinrich R, Aronheim A", "evidence": [ { "database": "iPTMnet", "id": "Q8WYK2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2-1" } ], "reference": [ { "type": "PubMed", "id": "11602244", "url": "https://glygen.org/publication/PubMed/11602244" } ] }, { "title": "Differential targeting of the stress mitogen-activated protein kinases to the c-Jun dimerization protein 2.", "journal": "The Biochemical journal", "date": "2002", "authors": "Katz S, Aronheim A", "evidence": [ { "database": "iPTMnet", "id": "Q8WYK2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2-1" } ], "reference": [ { "type": "PubMed", "id": "12225289", "url": "https://glygen.org/publication/PubMed/12225289" } ] }, { "title": "Phosphorylation of JDP2 on threonine-148 by the c-Jun N-terminal kinase targets it for proteosomal degradation.", "journal": "The Biochemical journal", "date": "2011", "authors": "Weidenfeld-Baranboim K, Koren L, Aronheim A", "evidence": [ { "database": "iPTMnet", "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2" } ], "reference": [ { "type": "PubMed", "id": "21463260", "url": "https://glygen.org/publication/PubMed/21463260" } ] }, { "title": "Ras inhibition boosts galectin-7 at the expense of galectin-1 to sensitize cells to apoptosis.", "journal": "Oncotarget", "date": "2013", "authors": "Barkan B, Cox AD, Kloog Y", "evidence": [ { "database": "iPTMnet", "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2" } ], "reference": [ { "type": "PubMed", "id": "23530091", "url": "https://glygen.org/publication/PubMed/23530091" } ] }, { "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": "iPTMnet", "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Phosphorylation of two eukaryotic transcription factors, Jun dimerization protein 2 and activation transcription factor 2, in Escherichia coli by Jun N-terminal kinase 1.", "journal": "Analytical biochemistry", "date": "2008", "authors": "Murata T, Shinozuka Y, Obata Y, Yokoyama KK", "evidence": [ { "database": "UniProtKB", "id": "Q8WYK2", "url": "https://www.uniprot.org/uniprotkb/Q8WYK2" }, { "database": "iPTMnet", "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2" } ], "reference": [ { "type": "PubMed", "id": "18307971", "url": "https://glygen.org/publication/PubMed/18307971" } ] } ], "crossref": [ { "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11602244", "url": "https://glygen.org/publication/PubMed/11602244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12225289", "url": "https://glygen.org/publication/PubMed/12225289", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WYK2", "url": "https://www.uniprot.org/uniprotkb/Q8WYK2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21463260", "url": "https://glygen.org/publication/PubMed/21463260", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23530091", "url": "https://glygen.org/publication/PubMed/23530091", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18307971", "url": "https://glygen.org/publication/PubMed/18307971", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LILMLNRHRPTCIVRTDSVK", "down_seq": "PESEGNPLLEQLEKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P45983-1", "kinase_gene_name": "MAPK8", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2" }, { "database": "PubMed", "id": "11602244", "url": "https://glygen.org/publication/PubMed/11602244" }, { "database": "PubMed", "id": "12225289", "url": "https://glygen.org/publication/PubMed/12225289" } ], "site_lbl": "Thr148" }, { "kinase_uniprot_canonical_ac": "P45984-1", "kinase_gene_name": "MAPK9", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2" }, { "database": "PubMed", "id": "11602244", "url": "https://glygen.org/publication/PubMed/11602244" }, { "database": "PubMed", "id": "12225289", "url": "https://glygen.org/publication/PubMed/12225289" } ], "site_lbl": "Thr148" }, { "kinase_uniprot_canonical_ac": "Q16539-1", "kinase_gene_name": "MAPK14", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2" }, { "database": "PubMed", "id": "11602244", "url": "https://glygen.org/publication/PubMed/11602244" }, { "database": "PubMed", "id": "12225289", "url": "https://glygen.org/publication/PubMed/12225289" } ], "site_lbl": "Thr148" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by MAPK8", "evidence": [ { "database": "UniProtKB", "id": "Q8WYK2", "url": "https://www.uniprot.org/uniprotkb/Q8WYK2" }, { "database": "iPTMnet", "id": "Q8WYK2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYK2" }, { "database": "PubMed", "id": "12225289", "url": "https://glygen.org/publication/PubMed/12225289" }, { "database": "PubMed", "id": "21463260", "url": "https://glygen.org/publication/PubMed/21463260" }, { "database": "PubMed", "id": "23530091", "url": "https://glygen.org/publication/PubMed/23530091" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18307971", "url": "https://glygen.org/publication/PubMed/18307971" } ], "site_lbl": "Thr148" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "148", "end_pos": "148" } ] } ], "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": 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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75022-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs564814709", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs564814709", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs564814709", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs564814709", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs564814709", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs564814709", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs564814709", "url": "http://gnomad.broadinstitute.org/awesome?query=rs564814709", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2078237883", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078237883", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2078237883", "url": "https://www.ensembl.org/id/rs2078237883", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GAYSKPTLSALPSPVVASGG", "down_seq": "MTLRCGSQKGYHHFVLMKEG", "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": "Asn139", "evidence": [ { "id": "O75022", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75022#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs564814709", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs564814709" }, { "id": "rs564814709", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs564814709" }, { "id": "rs564814709", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs564814709" }, { "id": "rs564814709", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs564814709" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NMT->KMT).", "chr_id": "19", "chr_pos": "54222069", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N139", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2078237883", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078237883" }, { "id": "rs2078237883", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2078237883" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NMT->SMT).", "chr_id": "19", "chr_pos": "54222070", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N139", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75022-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75022-1.141.141", "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": 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": "O75022-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "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": "O75022", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs75069054", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs75069054", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs75069054", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs75069054", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs75069054", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs75069054", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs75069054", "url": "http://gnomad.broadinstitute.org/awesome?query=rs75069054", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs75069054", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs75069054", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2078219463", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078219463", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2078219463", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2078219463#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LDSQQLHSRGFQALFPVGPV", "down_seq": "PSHRWRFTCYYYYTNTPWVW", "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": "Thr187", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "O75022", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022" }, { "id": "rs75069054", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs75069054" }, { "id": "rs75069054", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs75069054" }, { "id": "rs75069054", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs75069054" }, { "id": "rs75069054", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs75069054" }, { "id": "rs75069054", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs75069054" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); o-glyco-site-loss (T->N).", "chr_id": "19", "chr_pos": "54221926", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T187", "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: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: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", "ebi" ] }, { "evidence": [ { "id": "rs2078219463", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078219463" }, { "id": "rs2078219463", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2078219463#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": "19", "chr_pos": "54221927", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T187", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "O75022-1.204.204", "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": 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": "O75022-1.280.280", "start_pos": 280, "end_pos": 280, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs780449866", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780449866", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780449866", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780449866", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780449866", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780449866", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1323266560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1323266560", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1323266560", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1323266560#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GERDFLQRPGQQPQAGLSQA", "down_seq": "FTLGPVSPSNGGQYRCYGAH", "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": "Asn280", "evidence": [ { "id": "O75022", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75022#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs780449866", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780449866" }, { "id": "rs780449866", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780449866" }, { "id": "rs780449866", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780449866" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NFT->DFT).", "chr_id": "19", "chr_pos": "54221200", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N280", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1323266560", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1323266560" }, { "id": "rs1323266560", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1323266560#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NFT->SFT).", "chr_id": "19", "chr_pos": "54221199", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N280", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "O75022-1.294.294", "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": 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": "O75022-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1348200919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348200919", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1348200919", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1348200919", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs1348200919", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1348200919", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "O75022", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs759194325", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759194325", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759194325", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759194325", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759194325", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759194325", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs759194325", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs759194325", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1287351877", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1287351877", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1287351877", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1287351877", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FTLGPVSPSNGGQYRCYGAH", "down_seq": "LSSEWSAPSDPLNILMAGQI", "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": "Asn301", "evidence": [ { "id": "O75022", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75022#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1348200919", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348200919" }, { "id": "rs1348200919", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1348200919" }, { "id": "rs1348200919", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1348200919" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->HLS).", "chr_id": "19", "chr_pos": "54221137", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N301", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O75022", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022" }, { "id": "rs759194325", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759194325" }, { "id": "rs759194325", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759194325" }, { "id": "rs759194325", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759194325" }, { "id": "rs759194325", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs759194325" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLS->KLS).", "chr_id": "19", "chr_pos": "54221135", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N301", "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" ] }, { "evidence": [ { "id": "rs1287351877", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1287351877" }, { "id": "rs1287351877", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1287351877" } ], "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": "19", "chr_pos": "54221136", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N301", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1287351877", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1287351877" }, { "id": "rs1287351877", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1287351877" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->TLS).", "chr_id": "19", "chr_pos": "54221136", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N301", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O75022-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75022-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75022-1.304.304", "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": 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": 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": 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": "O75022-1.334.334", "start_pos": 334, "end_pos": 334, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "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": "O75022", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2147335337", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147335337", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147335337", "url": "https://www.ensembl.org/id/rs2147335337", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NILMAGQIYDTVSLSAQPGP", "down_seq": "VASGENVTLLCQSWWQFDTF", "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": "Thr334", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "O75022", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "19", "chr_pos": "54220785", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T334", "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": "rs2147335337", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147335337" }, { "id": "rs2147335337", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147335337" } ], "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": "19", "chr_pos": "54220785", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T334", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O75022-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75022-1.340.340", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O75022-1.342.342", "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": 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": "O75022-1.340.340", "start_pos": 340, "end_pos": 340, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs760034371", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760034371", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QIYDTVSLSAQPGPTVASGE", "down_seq": "VTLLCQSWWQFDTFLLTKEG", "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": "Asn340", "evidence": [ { "id": "O75022", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75022#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs760034371", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760034371" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVT->KVT).", "chr_id": "19", "chr_pos": "54220766", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N340", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O75022-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O75022-1.334.334", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75022-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75022-1.360.360", "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": "O75022-1.430.430", "start_pos": 430, "end_pos": 430, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "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": "PSEPLELVVSGHSGGSSLPP", "down_seq": "GPPSTPGLGRYLEVLIGVSV", "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": "Thr430", "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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "O75022-1.435.435", "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": "O75022-1.435.435", "start_pos": 435, "end_pos": 435, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "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": "rs1373930807", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1373930807", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1373930807", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1373930807#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ELVVSGHSGGSSLPPTGPPS", "down_seq": "PGLGRYLEVLIGVSVAFVLL", "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": "Thr435", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1373930807", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1373930807" }, { "id": "rs1373930807", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1373930807#frequency_tab" } ], "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": "19", "chr_pos": "54220160", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T435", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "O75022-1.430.430", "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": 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": "O75022-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1411410666", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1411410666", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1411410666", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1411410666", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GWSEPSDPLEMVMTGAYSKP", "down_seq": "LSALPSPVVASGGNMTLRCG", "snv": [ { "evidence": [ { "id": "rs1411410666", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1411410666" }, { "id": "rs1411410666", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1411410666" } ], "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 (TLS->NLS).", "chr_id": "19", "chr_pos": "54222112", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T125", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "O75022-1.139.139", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O75022-1.141.141", "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": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75022-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752162678", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752162678", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752162678", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752162678", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752162678", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752162678", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YSKPTLSALPSPVVASGGNM", "down_seq": "LRCGSQKGYHHFVLMKEGEH", "snv": [ { "evidence": [ { "id": "rs752162678", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752162678" }, { "id": "rs752162678", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752162678" }, { "id": "rs752162678", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752162678" } ], "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 (NMT->NMI).", "chr_id": "19", "chr_pos": "54222064", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T141", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O75022-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75022-1.139.139", "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": "O75022-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75022", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2078212869", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078212869", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2078212869", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2078212869", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "GPVTPSHRWRFTCYYYYTNT", "down_seq": "WVWSHPSDPLEILPSGVSRK", "snv": [ { "evidence": [ { "id": "O75022", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022" } ], "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 (NTP->NTS).", "chr_id": "19", "chr_pos": "54221876", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P204", "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": "rs2078212869", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078212869" }, { "id": "rs2078212869", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2078212869" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTP->NTT).", "chr_id": "19", "chr_pos": "54221876", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P204", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O75022-1.187.187", "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": 1 } ], "sort_fields": [ "subjects_tested", "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": "O75022-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1443163215", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443163215", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1443163215", "url": "https://www.ensembl.org/id/rs1443163215", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GVSRKPSLLTLQGPVLAPGQ", "down_seq": "LTLQCGSDVGYNRFVLYKEG", "snv": [ { "evidence": [ { "id": "rs1443163215", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443163215" }, { "id": "rs1443163215", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1443163215" } ], "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 (SLT->NLT).", "chr_id": "19", "chr_pos": "54221319", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S240", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "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": "O75022-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2078132698", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078132698", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2078132698", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2078132698", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "AGLSQANFTLGPVSPSNGGQ", "down_seq": "RCYGAHNLSSEWSAPSDPLN", "snv": [ { "evidence": [ { "id": "rs2078132698", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078132698" }, { "id": "rs2078132698", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2078132698" } ], "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 (YRC->NRC).", "chr_id": "19", "chr_pos": "54221158", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y294", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75022-1.280.280", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O75022-1.301.301", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75022-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75022-1.304.304", "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": "O75022-1.303.303", "start_pos": 303, "end_pos": 303, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1600895876", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600895876", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600895876", "url": "https://www.ensembl.org/id/rs1600895876", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGPVSPSNGGQYRCYGAHNL", "down_seq": "SEWSAPSDPLNILMAGQIYD", "snv": [ { "evidence": [ { "id": "rs1600895876", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600895876" }, { "id": "rs1600895876", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600895876" } ], "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 (NLS->NLA).", "chr_id": "19", "chr_pos": "54221131", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S303", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O75022-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75022-1.301.301", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75022-1.304.304", "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": "O75022-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75022", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GPVSPSNGGQYRCYGAHNLS", "down_seq": "EWSAPSDPLNILMAGQIYDT", "snv": [ { "evidence": [ { "id": "O75022", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "54221127", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S304", "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: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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O75022-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75022-1.301.301", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75022-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75022-1.324.324", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "O75022-1.324.324", "start_pos": 324, "end_pos": 324, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1449319009", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1449319009", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1449319009", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1449319009#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1449319009", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1449319009", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SEWSAPSDPLNILMAGQIYD", "down_seq": "VSLSAQPGPTVASGENVTLL", "snv": [ { "evidence": [ { "id": "rs1449319009", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1449319009" }, { "id": "rs1449319009", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1449319009#frequency_tab" }, { "id": "rs1449319009", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1449319009" } ], "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": "19", "chr_pos": "54220815", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T324", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75022-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75022-1.334.334", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O75022-1.340.340", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O75022-1.342.342", "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": "O75022-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771442791", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771442791", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771442791", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771442791", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771442791", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771442791", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YDTVSLSAQPGPTVASGENV", "down_seq": "LLCQSWWQFDTFLLTKEGAA", "snv": [ { "evidence": [ { "id": "rs771442791", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771442791" }, { "id": "rs771442791", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771442791" }, { "id": "rs771442791", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771442791" } ], "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 (NVT->NVI).", "chr_id": "19", "chr_pos": "54220761", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T342", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O75022-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "O75022-1.334.334", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75022-1.340.340", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O75022-1.360.360", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75022-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75022", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "NVTLLCQSWWQFDTFLLTKE", "down_seq": "AAHPPLRLRSMYGAHKYQAE", "snv": [ { "evidence": [ { "id": "O75022", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75022" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "54220707", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G360", "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: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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75022-1.340.340", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "O75022-1.342.342", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "O75022-1.530.530", "start_pos": 530, "end_pos": 530, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751447602", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751447602", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751447602", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751447602", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751447602", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751447602", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EENLYAAVKDTQSEDRVELD", "down_seq": "QSPHDEDPQAVTYAPVKHSS", "snv": [ { "evidence": [ { "id": "rs751447602", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751447602" }, { "id": "rs751447602", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751447602" }, { "id": "rs751447602", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751447602" } ], "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": "19", "chr_pos": "54218365", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S530", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "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": "O75022-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1156552324", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1156552324", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1156552324", "url": "https://www.ensembl.org/id/rs1156552324", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "EAQEYRLHKEGSPEPLDRNN", "down_seq": "LEPKNKARFSIPSMTEHHAG", "snv": [ { "evidence": [ { "id": "rs1156552324", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1156552324" }, { "id": "rs1156552324", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1156552324" } ], "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": "19", "chr_pos": "54222413", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P74", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "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": "O75022-1.595.595", "start_pos": 595, "end_pos": 595, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "EEDRQMDTEAAASEASQDVT", "down_seq": "AQLHSLTLRRKATEPPPSQE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by LYN", "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "site_lbl": "Tyr595" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "O75022-1.602.602", "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": "O75022-1.602.602", "start_pos": 602, "end_pos": 602, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "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": "O75022", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75022" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "O75022", "url": "https://www.iedb.org/epitope/O75022", "database": "IEDB", "categories": [ "Other" ] }, { "id": "O75022", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75022", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TEAAASEASQDVTYAQLHSL", "down_seq": "LRRKATEPPPSQEGEPPAEP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "O75022", "url": "https://www.iedb.org/epitope/O75022" }, { "database": "iPTMnet", "id": "O75022", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75022" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Thr602" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O75022-1.595.595", "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": "O75022-1.625.625", "start_pos": 625, "end_pos": 625, "uniprot_canonical_ac": "O75022-1", "length": 631, "uniprot_id": "LIRB3_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 3", "refseq_ac": "", "refseq_name": "", "gene_name": "LILRB3", "gene_names_uniprotkb": "LILRB3; ILT5; LIR3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RKATEPPPSQEGEPPAEPSI", "down_seq": "ATLAIH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by LYN", "evidence": [ { "database": "UniProtKB", "id": "O75022", "url": "https://www.uniprot.org/uniprotkb/O75022" } ], "site_lbl": "Tyr625" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "595", "end_pos": "595" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "625", "end_pos": "625" } ] } ], "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": "Q6PI73-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs761640789", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761640789", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761640789", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs761640789", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs761640789", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761640789", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761640789", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761640789", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs761640789", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs761640789", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1459556065", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1459556065", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1459556065", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1459556065", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GFYNKPTLSALPSPVVASGG", "down_seq": "MTLRCGSQKGYHHFVLMKEG", "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": "Asn139", "evidence": [ { "id": "Q6PI73", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q6PI73#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs761640789", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761640789" }, { "id": "rs761640789", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs761640789" }, { "id": "rs761640789", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761640789" }, { "id": "rs761640789", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761640789" }, { "id": "rs761640789", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs761640789" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NMT->KMT).", "chr_id": "19", "chr_pos": "54241817", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N139", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1459556065", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1459556065" }, { "id": "rs1459556065", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1459556065" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NMT->SMT).", "chr_id": "19", "chr_pos": "54241818", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N139", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6PI73-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6PI73-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6PI73-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6PI73-1.149.149", "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": 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": "Q6PI73-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "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": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LDSQQLHSGGFQALFPVGPV", "down_seq": "PSHRWRFTCYYYYTNTPRVW", "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": "Thr187", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "9251", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "19", "chr_pos": "54241674", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T187", "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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q6PI73-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6PI73-1.205.205", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q6PI73-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1460675378", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1460675378", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1460675378", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1460675378#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1460675378", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1460675378", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1460675378", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1460675378", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1354286824", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1354286824", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1354286824", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1354286824", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1481861231", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1481861231", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1481861231", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1481861231#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FTLGPVSPSHGGQYRCYGAH", "down_seq": "LSSEWSAPSDPLNILMAGQI", "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": "Asn301", "evidence": [ { "id": "Q6PI73", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q6PI73#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" }, { "id": "rs1460675378", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1460675378" }, { "id": "rs1460675378", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1460675378#frequency_tab" }, { "id": "rs1460675378", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1460675378" }, { "id": "rs1460675378", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1460675378" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLS->DLS).", "chr_id": "19", "chr_pos": "54240885", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N301", "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" ] }, { "evidence": [ { "id": "rs1460675378", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1460675378" }, { "id": "rs1460675378", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1460675378#frequency_tab" }, { "id": "rs1460675378", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1460675378" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->HLS).", "chr_id": "19", "chr_pos": "54240885", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N301", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1354286824", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1354286824" }, { "id": "rs1354286824", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1354286824" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->KLS).", "chr_id": "19", "chr_pos": "54240883", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N301", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1481861231", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1481861231" }, { "id": "rs1481861231", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1481861231#frequency_tab" } ], "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": "19", "chr_pos": "54240884", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N301", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6PI73-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6PI73-1.303.303", "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": 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": 1 } ], "sort_fields": [ "subjects_tested", "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": 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": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6PI73-1.334.334", "start_pos": 334, "end_pos": 334, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "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": "rs1208945700", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1208945700", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1208945700", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1208945700", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NILMAGQIYDTVSLSAQPGP", "down_seq": "VASGENVTLLCQSRGYFDTF", "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": "Thr334", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1208945700", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1208945700" }, { "id": "rs1208945700", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1208945700" } ], "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": "19", "chr_pos": "54240531", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T334", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6PI73-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6PI73-1.340.340", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6PI73-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6PI73-1.342.342", "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": "Q6PI73-1.340.340", "start_pos": 340, "end_pos": 340, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs773243204", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773243204", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773243204", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773243204", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs773243204", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773243204", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773243204", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773243204#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773243204", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773243204", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QIYDTVSLSAQPGPTVASGE", "down_seq": "VTLLCQSRGYFDTFLLTKEG", "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": "Asn340", "evidence": [ { "id": "Q6PI73", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q6PI73#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs773243204", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773243204" }, { "id": "rs773243204", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773243204" }, { "id": "rs773243204", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773243204" }, { "id": "rs773243204", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773243204#frequency_tab" }, { "id": "rs773243204", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773243204" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVT->KVT).", "chr_id": "19", "chr_pos": "54240512", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N340", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6PI73-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6PI73-1.334.334", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6PI73-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6PI73-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6PI73-1.360.360", "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": "Q6PI73-1.435.435", "start_pos": 435, "end_pos": 435, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "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": "ELMVSGHSGGSSLPPTGPPS", "down_seq": "PASHAKDYTVENLIRMGMAG", "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": "Thr435", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q6PI73-1.442.442", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6PI73-1.449.449", "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": "Q6PI73-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "RCHYYSSAGWSEPSDPLELV", "down_seq": "TGFYNKPTLSALPSPVVASG", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "18", "frequency": "0.2", "sequence_org": "M", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: patient count (18/9251).", "chr_id": "19", "chr_pos": "54242031", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "M117", "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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q6PI73-1.124.124", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q6PI73-1.124.124", "start_pos": 124, "end_pos": 124, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1200919201", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1200919201", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1200919201", "url": "https://www.ensembl.org/id/rs1200919201", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AGWSEPSDPLELVMTGFYNK", "down_seq": "TLSALPSPVVASGGNMTLRC", "snv": [ { "evidence": [ { "id": "rs1200919201", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1200919201" }, { "id": "rs1200919201", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1200919201" } ], "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": "19", "chr_pos": "54241864", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P124", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q6PI73-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6PI73-1.139.139", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6PI73-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6PI73-1.143.143", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6PI73-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs765787230", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765787230", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765787230", "url": "https://www.ensembl.org/id/rs765787230", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YNKPTLSALPSPVVASGGNM", "down_seq": "LRCGSQKGYHHFVLMKEGEH", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" }, { "id": "rs765787230", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765787230" }, { "id": "rs765787230", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs765787230" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NMT->NMI).", "chr_id": "19", "chr_pos": "54241812", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T141", "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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6PI73-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6PI73-1.139.139", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6PI73-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6PI73-1.149.149", "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": "Q6PI73-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KPTLSALPSPVVASGGNMTL", "down_seq": "CGSQKGYHHFVLMKEGEHQL", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "54241806", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R143", "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: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: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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6PI73-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6PI73-1.139.139", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6PI73-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6PI73-1.149.149", "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": "Q6PI73-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LPSPVVASGGNMTLRCGSQK", "down_seq": "YHHFVLMKEGEHQLPRTLDS", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "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": "19", "chr_pos": "54241789", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G149", "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: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: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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q6PI73-1.139.139", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6PI73-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6PI73-1.143.143", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6PI73-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1295193830", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1295193830", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1295193830", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1295193830#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1295193830", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1295193830", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "GPVTPSHRWRFTCYYYYTNT", "down_seq": "RVWSHPSDPLEILPSGVSRK", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "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 (NTP->NTS).", "chr_id": "19", "chr_pos": "54241624", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P204", "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": "rs1295193830", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1295193830" }, { "id": "rs1295193830", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1295193830#frequency_tab" }, { "id": "rs1295193830", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1295193830" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTP->NTT).", "chr_id": "19", "chr_pos": "54241624", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P204", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6PI73-1.187.187", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6PI73-1.205.205", "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": 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": "Q6PI73-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PVTPSHRWRFTCYYYYTNTP", "down_seq": "VWSHPSDPLEILPSGVSRKP", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "54241621", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R205", "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: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: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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q6PI73-1.187.187", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6PI73-1.204.204", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q6PI73-1.21.21", "start_pos": 21, "end_pos": 21, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MTPALTALLCLGLSLGPRTR", "down_seq": "QAGPFPKPTLWAEPGSVISW", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "4", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "19", "chr_pos": "54242528", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V21", "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: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: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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "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": "Q6PI73-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2078750680", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078750680", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2078750680", "url": "https://www.ensembl.org/id/rs2078750680", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2078750680", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2078750680", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GVSRKPSLLTLQGPVLAPGQ", "down_seq": "LTLQCGSDVGYDRFVLYKEG", "snv": [ { "evidence": [ { "id": "rs2078750680", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2078750680" }, { "id": "rs2078750680", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2078750680" }, { "id": "rs2078750680", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2078750680" } ], "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 (SLT->NLT).", "chr_id": "19", "chr_pos": "54241067", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S240", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "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": "Q6PI73-1.267.267", "start_pos": 267, "end_pos": 267, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SDVGYDRFVLYKEGERDFLQ", "down_seq": "PGQQPQAGLSQANFTLGPVS", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "54240986", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R267", "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: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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "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": "Q6PI73-1.290.290", "start_pos": 290, "end_pos": 290, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "QQPQAGLSQANFTLGPVSPS", "down_seq": "GGQYRCYGAHNLSSEWSAPS", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "27", "frequency": "0.3", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: patient count (27/9251).", "chr_id": "19", "chr_pos": "54240918", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H290", "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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q6PI73-1.301.301", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6PI73-1.303.303", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q6PI73-1.303.303", "start_pos": 303, "end_pos": 303, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1357703940", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357703940", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1357703940", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1357703940", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1357703940", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1357703940", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGPVSPSHGGQYRCYGAHNL", "down_seq": "SEWSAPSDPLNILMAGQIYD", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" }, { "id": "rs1357703940", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357703940" }, { "id": "rs1357703940", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1357703940" }, { "id": "rs1357703940", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1357703940" } ], "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 (NLS->NLF).", "chr_id": "19", "chr_pos": "54240878", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S303", "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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6PI73-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6PI73-1.301.301", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6PI73-1.323.323", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q6PI73-1.323.323", "start_pos": 323, "end_pos": 323, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SSEWSAPSDPLNILMAGQIY", "down_seq": "TVSLSAQPGPTVASGENVTL", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "D", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "19", "chr_pos": "54240565", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "D323", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6PI73-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6PI73-1.334.334", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6PI73-1.340.340", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6PI73-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6PI73-1.342.342", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q6PI73-1.341.341", "start_pos": 341, "end_pos": 341, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "IYDTVSLSAQPGPTVASGEN", "down_seq": "TLLCQSRGYFDTFLLTKEGA", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "4", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "54240511", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V341", "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: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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q6PI73-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q6PI73-1.334.334", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6PI73-1.340.340", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6PI73-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6PI73-1.360.360", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q6PI73-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778854296", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778854296", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778854296", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778854296", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778854296", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778854296", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YDTVSLSAQPGPTVASGENV", "down_seq": "LLCQSRGYFDTFLLTKEGAA", "snv": [ { "evidence": [ { "id": "rs778854296", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778854296" }, { "id": "rs778854296", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778854296" }, { "id": "rs778854296", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778854296" } ], "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 (NVT->NVI).", "chr_id": "19", "chr_pos": "54240507", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T342", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6PI73-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6PI73-1.334.334", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6PI73-1.340.340", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6PI73-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6PI73-1.360.360", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6PI73-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "NVTLLCQSRGYFDTFLLTKE", "down_seq": "AAHPPLRLRSMYGAHKYQAE", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "54240453", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G360", "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: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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6PI73-1.340.340", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q6PI73-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q6PI73-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6PI73-1.367.367", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q6PI73-1.367.367", "start_pos": 367, "end_pos": 367, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SRGYFDTFLLTKEGAAHPPL", "down_seq": "LRSMYGAHKYQAEFPMSPVT", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "54240432", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R367", "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" } ] }, { "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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q6PI73-1.360.360", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q6PI73-1.391.391", "start_pos": 391, "end_pos": 391, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MYGAHKYQAEFPMSPVTSAH", "down_seq": "GTYRCYGSYSSNPHLLSFPS", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "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": "19", "chr_pos": "54240360", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A391", "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: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: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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "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": "Q6PI73-1.442.442", "start_pos": 442, "end_pos": 442, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SGGSSLPPTGPPSTPASHAK", "down_seq": "YTVENLIRMGMAGLVLVFLG", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "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 (DYT->NYT).", "chr_id": "19", "chr_pos": "54239075", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D442", "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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q6PI73-1.435.435", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6PI73-1.449.449", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6PI73-1.449.449", "start_pos": 449, "end_pos": 449, "uniprot_canonical_ac": "Q6PI73-1", "length": 481, "uniprot_id": "LIRA6_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily A member 6", "refseq_ac": "NP_001347096", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily A member 6 isoform 2 precursor", "gene_name": "LILRA6", "gene_names_uniprotkb": "LILRA6; ILT8", "gene_names_refseq": "CD85b; ILT-8; ILT5; ILT8; LILRA6; LILRB6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6PI73", "url": "https://www.uniprot.org/uniprotkb/Q6PI73" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6PI73", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "PTGPPSTPASHAKDYTVENL", "down_seq": "RMGMAGLVLVFLGILLFEAQ", "snv": [ { "evidence": [ { "id": "Q6PI73", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6PI73" } ], "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 (NLI->NLT).", "chr_id": "19", "chr_pos": "54239053", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "I449", "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": "139", "end_pos": "139" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "435", "end_pos": "435" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "449", "end_pos": "449" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6PI73-1.435.435", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q6PI73-1.442.442", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q5VT66-1.166.166", "start_pos": 166, "end_pos": 166, "uniprot_canonical_ac": "Q5VT66-1", "length": 337, "uniprot_id": "MARC1_HUMAN", "protein_name": "Mitochondrial amidoxime-reducing component 1", "refseq_ac": "NP_073583", "refseq_name": "mitochondrial amidoxime-reducing component 1 precursor", "gene_name": "MTARC1", "gene_names_uniprotkb": "MTARC1; MARC1; MOSC1", "gene_names_refseq": "MARC1; MOSC1; MTARC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VT66", "url": "https://www.uniprot.org/uniprotkb/Q5VT66" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VT66", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VT66", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VHKCRVHGLEIEGRDCGEAT", "down_seq": "QWITSFLKSQPYRLVHFEPH", "snv": [ { "evidence": [ { "id": "Q5VT66", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VT66" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "220796689", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A166", "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: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": "166", "end_pos": "166" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "305", "end_pos": "305" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] } ], "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": "Q5VT66-1.190.190", "start_pos": 190, "end_pos": 190, "uniprot_canonical_ac": "Q5VT66-1", "length": 337, "uniprot_id": "MARC1_HUMAN", "protein_name": "Mitochondrial amidoxime-reducing component 1", "refseq_ac": "NP_073583", "refseq_name": "mitochondrial amidoxime-reducing component 1 precursor", "gene_name": "MTARC1", "gene_names_uniprotkb": "MTARC1; MARC1; MOSC1", "gene_names_refseq": "MARC1; MOSC1; MTARC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VT66", "url": "https://www.uniprot.org/uniprotkb/Q5VT66" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VT66", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VT66", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TSFLKSQPYRLVHFEPHMRP", "down_seq": "RPHQIADLFRPKDQIAYSDT", "snv": [ { "evidence": [ { "id": "Q5VT66", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VT66" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "220796762", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R190", "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": "snv", "site_list": [ { "start_pos": "166", "end_pos": "166" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "305", "end_pos": "305" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] } ], "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": "Q5VT66-1.247.247", "start_pos": 247, "end_pos": 247, "uniprot_canonical_ac": "Q5VT66-1", "length": 337, "uniprot_id": "MARC1_HUMAN", "protein_name": "Mitochondrial amidoxime-reducing component 1", "refseq_ac": "NP_073583", "refseq_name": "mitochondrial amidoxime-reducing component 1 precursor", "gene_name": "MTARC1", "gene_names_uniprotkb": "MTARC1; MARC1; MOSC1", "gene_names_refseq": "MARC1; MOSC1; MTARC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VT66", "url": "https://www.uniprot.org/uniprotkb/Q5VT66" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VT66", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VT66", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RLEKKVKATNFRPNIVISGC", "down_seq": "VYAEDSWDELLIGDVELKRV", "snv": [ { "evidence": [ { "id": "Q5VT66", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VT66" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "220798000", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D247", "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": "166", "end_pos": "166" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "305", "end_pos": "305" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] } ], "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": "Q5VT66-1.305.305", "start_pos": 305, "end_pos": 305, "uniprot_canonical_ac": "Q5VT66-1", "length": 337, "uniprot_id": "MARC1_HUMAN", "protein_name": "Mitochondrial amidoxime-reducing component 1", "refseq_ac": "NP_073583", "refseq_name": "mitochondrial amidoxime-reducing component 1 precursor", "gene_name": "MTARC1", "gene_names_uniprotkb": "MTARC1; MARC1; MOSC1", "gene_names_refseq": "MARC1; MOSC1; MTARC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VT66", "url": "https://www.uniprot.org/uniprotkb/Q5VT66" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VT66", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VT66", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MSRKEPLETLKSYRQCDPSE", "down_seq": "KLYGKSPLFGQYFVLENPGT", "snv": [ { "evidence": [ { "id": "Q5VT66", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VT66" } ], "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 (3).", "chr_id": "1", "chr_pos": "220813318", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R305", "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: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": "166", "end_pos": "166" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "305", "end_pos": "305" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] } ], "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": "Q5VT66-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "Q5VT66-1", "length": 337, "uniprot_id": "MARC1_HUMAN", "protein_name": "Mitochondrial amidoxime-reducing component 1", "refseq_ac": "NP_073583", "refseq_name": "mitochondrial amidoxime-reducing component 1 precursor", "gene_name": "MTARC1", "gene_names_uniprotkb": "MTARC1; MARC1; MOSC1", "gene_names_refseq": "MARC1; MOSC1; MTARC1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VT66", "url": "https://www.uniprot.org/uniprotkb/Q5VT66" } ], "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": "Q5VT66-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT66-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q5VT66", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT66", "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": "MGAAGSSALARFVLLAQ", "down_seq": "RPGWLGVAALGLTAVALGAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q5VT66", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT66" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser18" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "166", "end_pos": "166" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "305", "end_pos": "305" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] } ], "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": "Q99706-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "Q99706-1", "length": 377, "uniprot_id": "KI2L4_HUMAN", "protein_name": "Killer cell immunoglobulin-like receptor 2DL4", "refseq_ac": "NP_001074239", "refseq_name": "killer cell immunoglobulin-like receptor 2DL4 isoform c precursor", "gene_name": "KIR2DL4", "gene_names_uniprotkb": "KIR2DL4; CD158D; KIR103AS; LOC112268354; LOC124900568", "gene_names_refseq": "CD158D; G9P; KIR-103AS; KIR-2DL4; KIR103AS; KIR103; KIR2DL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "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": "Q99706", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LVIMVTGLYEKPSLTARPGP", "down_seq": "VRAGENVTLSCSSQSSFDIY", "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": "Thr135", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "Q99706", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706" } ], "glycoeffect": [ "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: o-glyco-site-loss (T->M).", "chr_id": "19", "chr_pos": "54805993", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T135", "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": "135", "end_pos": "135" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "246", "end_pos": "247" } ] }, { "type": "snv", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "54", "end_pos": "54" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q99706-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q99706-1.141.141", "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": 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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q99706-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "Q99706-1", "length": 377, "uniprot_id": "KI2L4_HUMAN", "protein_name": "Killer cell immunoglobulin-like receptor 2DL4", "refseq_ac": "NP_001074239", "refseq_name": "killer cell immunoglobulin-like receptor 2DL4 isoform c precursor", "gene_name": "KIR2DL4", "gene_names_uniprotkb": "KIR2DL4; CD158D; KIR103AS; LOC112268354; LOC124900568", "gene_names_refseq": "CD158D; G9P; KIR-103AS; KIR-2DL4; KIR103AS; KIR103; KIR2DL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "3WYR", "url": "https://www.rcsb.org/structure/3WYR", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "3WYR|B|118", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "3WYR|A|118", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GLYEKPSLTARPGPTVRAGE", "down_seq": "VTLSCSSQSSFDIYHLSREG", "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=3WYR&bu=0&command=select+.B:118;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn141", "evidence": [ { "id": "Q99706", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q99706#ptm_processing" }, { "id": "3WYR", "database": "PDB", "url": "https://www.rcsb.org/structure/3WYR" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "246", "end_pos": "247" } ] }, { "type": "snv", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "54", "end_pos": "54" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q99706-1.135.135", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q99706-1.137.137", "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": "Q99706-1.175.175", "start_pos": 175, "end_pos": 175, "uniprot_canonical_ac": "Q99706-1", "length": 377, "uniprot_id": "KI2L4_HUMAN", "protein_name": "Killer cell immunoglobulin-like receptor 2DL4", "refseq_ac": "NP_001074239", "refseq_name": "killer cell immunoglobulin-like receptor 2DL4 isoform c precursor", "gene_name": "KIR2DL4", "gene_names_uniprotkb": "KIR2DL4; CD158D; KIR103AS; LOC112268354; LOC124900568", "gene_names_refseq": "CD158D; G9P; KIR-103AS; KIR-2DL4; KIR103AS; KIR103; KIR2DL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YHLSREGEAHELRLPAVPSI", "down_seq": "GTFQADFPLGPATHGETYRC", "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": "Asn175", "evidence": [ { "id": "Q99706", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q99706#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "246", "end_pos": "247" } ] }, { "type": "snv", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "54", "end_pos": "54" } ] } ], "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": "Q99706-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "Q99706-1", "length": 377, "uniprot_id": "KI2L4_HUMAN", "protein_name": "Killer cell immunoglobulin-like receptor 2DL4", "refseq_ac": "NP_001074239", "refseq_name": "killer cell immunoglobulin-like receptor 2DL4 isoform c precursor", "gene_name": "KIR2DL4", "gene_names_uniprotkb": "KIR2DL4; CD158D; KIR103AS; LOC112268354; LOC124900568", "gene_names_refseq": "CD158D; G9P; KIR-103AS; KIR-2DL4; KIR103AS; KIR103; KIR2DL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "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": "PSDPLPVSVTGNPSSSWPSP", "down_seq": "EPSFKTGIARHLHAVIRYSV", "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": "Thr229", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "246", "end_pos": "247" } ] }, { "type": "snv", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "54", "end_pos": "54" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q99706-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q99706-1.246.247", "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": 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": "Q99706-1.88.88", "start_pos": 88, "end_pos": 88, "uniprot_canonical_ac": "Q99706-1", "length": 377, "uniprot_id": "KI2L4_HUMAN", "protein_name": "Killer cell immunoglobulin-like receptor 2DL4", "refseq_ac": "NP_001074239", "refseq_name": "killer cell immunoglobulin-like receptor 2DL4 isoform c precursor", "gene_name": "KIR2DL4", "gene_names_uniprotkb": "KIR2DL4; CD158D; KIR103AS; LOC112268354; LOC124900568", "gene_names_refseq": "CD158D; G9P; KIR-103AS; KIR-2DL4; KIR103AS; KIR103; KIR2DL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "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": "VPVPELYNRIFWNSFLISPV", "down_seq": "PAHAGTYRCRGFHPHSPTEW", "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": "Thr88", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "246", "end_pos": "247" } ] }, { "type": "snv", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "54", "end_pos": "54" } ] } ], "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": "Q99706-1.246.247", "start_pos": 246, "end_pos": 247, "uniprot_canonical_ac": "Q99706-1", "length": 377, "uniprot_id": "KI2L4_HUMAN", "protein_name": "Killer cell immunoglobulin-like receptor 2DL4", "refseq_ac": "NP_001074239", "refseq_name": "killer cell immunoglobulin-like receptor 2DL4 isoform c precursor", "gene_name": "KIR2DL4", "gene_names_uniprotkb": "KIR2DL4; CD158D; KIR103AS; LOC112268354; LOC124900568", "gene_names_refseq": "CD158D; G9P; KIR-103AS; KIR-2DL4; KIR103AS; KIR103; KIR2DL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Activation of NK cells by an endocytosed receptor for soluble HLA-G.", "journal": "PLoS biology", "date": "2006", "authors": "Rajagopalan S, Bryceson YT, Kuppusamy SP, Geraghty DE, van der Meer A, Joosten I, Long EO", "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "reference": [ { "type": "PubMed", "id": "16366734", "url": "https://glygen.org/publication/PubMed/16366734" } ] } ], "crossref": [ { "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16366734", "url": "https://glygen.org/publication/PubMed/16366734", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "RY", "start_aa": "R", "up_seq": "PSPTEPSFKTGIARHLHAVI", "down_seq": "SVAIILFTILPFFLLHRWCS", "mutagenesis": [ { "sequence_org": "RY", "sequence_mut": "GT", "comment": "Does not affect targeting to the endosomal compartment.", "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" }, { "database": "PubMed", "id": "16366734", "url": "https://glygen.org/publication/PubMed/16366734" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "246", "end_pos": "247" } ] }, { "type": "snv", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "54", "end_pos": "54" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q99706-1.229.229", "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": "Q99706-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "Q99706-1", "length": 377, "uniprot_id": "KI2L4_HUMAN", "protein_name": "Killer cell immunoglobulin-like receptor 2DL4", "refseq_ac": "NP_001074239", "refseq_name": "killer cell immunoglobulin-like receptor 2DL4 isoform c precursor", "gene_name": "KIR2DL4", "gene_names_uniprotkb": "KIR2DL4; CD158D; KIR103AS; LOC112268354; LOC124900568", "gene_names_refseq": "CD158D; G9P; KIR-103AS; KIR-2DL4; KIR103AS; KIR103; KIR2DL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q99706", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IMVTGLYEKPSLTARPGPTV", "down_seq": "AGENVTLSCSSQSSFDIYHL", "snv": [ { "evidence": [ { "id": "Q99706", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "54805999", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R137", "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: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: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": "135", "end_pos": "135" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "246", "end_pos": "247" } ] }, { "type": "snv", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "54", "end_pos": "54" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q99706-1.135.135", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q99706-1.141.141", "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": "Q99706-1.219.219", "start_pos": 219, "end_pos": 219, "uniprot_canonical_ac": "Q99706-1", "length": 377, "uniprot_id": "KI2L4_HUMAN", "protein_name": "Killer cell immunoglobulin-like receptor 2DL4", "refseq_ac": "NP_001074239", "refseq_name": "killer cell immunoglobulin-like receptor 2DL4 isoform c precursor", "gene_name": "KIR2DL4", "gene_names_uniprotkb": "KIR2DL4; CD158D; KIR103AS; LOC112268354; LOC124900568", "gene_names_refseq": "CD158D; G9P; KIR-103AS; KIR-2DL4; KIR103AS; KIR103; KIR2DL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q99706", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "FHGSPYEWSDPSDPLPVSVT", "down_seq": "NPSSSWPSPTEPSFKTGIAR", "snv": [ { "evidence": [ { "id": "Q99706", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "54806244", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G219", "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: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: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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "246", "end_pos": "247" } ] }, { "type": "snv", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "54", "end_pos": "54" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q99706-1.229.229", "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": "Q99706-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "Q99706-1", "length": 377, "uniprot_id": "KI2L4_HUMAN", "protein_name": "Killer cell immunoglobulin-like receptor 2DL4", "refseq_ac": "NP_001074239", "refseq_name": "killer cell immunoglobulin-like receptor 2DL4 isoform c precursor", "gene_name": "KIR2DL4", "gene_names_uniprotkb": "KIR2DL4; CD158D; KIR103AS; LOC112268354; LOC124900568", "gene_names_refseq": "CD158D; G9P; KIR-103AS; KIR-2DL4; KIR103AS; KIR103; KIR2DL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q99706", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KPFCSAWPSAVVPQGGHVTL", "down_seq": "CHYRRGFNIFTLYKKDGVPV", "snv": [ { "evidence": [ { "id": "Q99706", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "54804865", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R50", "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: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": "135", "end_pos": "135" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "246", "end_pos": "247" } ] }, { "type": "snv", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "54", "end_pos": "54" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q99706-1.54.54", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q99706-1.54.54", "start_pos": 54, "end_pos": 54, "uniprot_canonical_ac": "Q99706-1", "length": 377, "uniprot_id": "KI2L4_HUMAN", "protein_name": "Killer cell immunoglobulin-like receptor 2DL4", "refseq_ac": "NP_001074239", "refseq_name": "killer cell immunoglobulin-like receptor 2DL4 isoform c precursor", "gene_name": "KIR2DL4", "gene_names_uniprotkb": "KIR2DL4; CD158D; KIR103AS; LOC112268354; LOC124900568", "gene_names_refseq": "CD158D; G9P; KIR-103AS; KIR-2DL4; KIR103AS; KIR103; KIR2DL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99706", "url": "https://www.uniprot.org/uniprotkb/Q99706" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q99706", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SAWPSAVVPQGGHVTLRCHY", "down_seq": "RGFNIFTLYKKDGVPVPELY", "snv": [ { "evidence": [ { "id": "Q99706", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706" } ], "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": "19", "chr_pos": "54804876", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R54", "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: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": "Q99706", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99706" } ], "glycoeffect": [], "subjects_tested": "1773", "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": "54804877", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R54", "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: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": "135", "end_pos": "135" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "88", "end_pos": "88" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "246", "end_pos": "247" } ] }, { "type": "snv", "site_list": [ { "start_pos": "135", "end_pos": "135" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "54", "end_pos": "54" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q99706-1.50.50", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_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": "Q6ZN17-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "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": "Q6ZN17", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZN17" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZN17", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZN17" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZN17", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZN17", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "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": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q6ZN17", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZN17" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q6ZN17-1.3.3", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZN17-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN17", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN17", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "ASSTKSSIAPEEQSKKGPSV", "down_seq": "KRKKT", "snv": [ { "evidence": [ { "id": "Q6ZN17", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN17" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "105078763", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q245", "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: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": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q6ZN17-1.243.243", "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": "Q6ZN17-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZN17", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN17", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MA", "down_seq": "GGASKGGGEEPGKLPEPAEE", "snv": [ { "evidence": [ { "id": "Q6ZN17", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZN17" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "104957257", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E3", "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: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": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q6ZN17-1.0.0", "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": "Q6ZN17-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "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": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" }, { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q6ZN17-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "Q6ZN17-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FTFKKSSKGLESIRVTGPGG", "down_seq": "PCLGSERRPKGKTLQKRKPK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Ser105" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q6ZN17-1.96.96", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6ZN17-1.110.110", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6ZN17-1.118.118", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZN17-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "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": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" }, { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSKGLESIRVTGPGGSPCLG", "down_seq": "ERRPKGKTLQKRKPKGDRCY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "site_lbl": "Ser110" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6ZN17-1.96.96", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6ZN17-1.105.105", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6ZN17-1.118.118", "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": "Q6ZN17-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The KRAS/Lin28B axis maintains stemness of pancreatic cancer cells via the let-7i/TET3 pathway.", "journal": "Molecular oncology", "date": "2021-01", "authors": "Liu Yawen, Wang Dawei, Zhou Meng, Chen Hui, Wang Huizhi, Min Jingyu, Chen Jiaxi, Wu Shuhui, Ni Xiufan, Zhang Youli, Gong Aihua, Xu Min", "evidence": [ { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "reference": [ { "type": "PubMed", "id": "33107691", "url": "https://glygen.org/publication/PubMed/33107691" } ] } ], "crossref": [ { "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33107691", "url": "https://glygen.org/publication/PubMed/33107691", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RVTGPGGSPCLGSERRPKGK", "down_seq": "LQKRKPKGDRCYNCGGLDHH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" }, { "database": "PubMed", "id": "33107691", "url": "https://glygen.org/publication/PubMed/33107691" } ], "site_lbl": "Thr118" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6ZN17-1.105.105", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6ZN17-1.110.110", "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": "Q6ZN17-1.203.203", "start_pos": 203, "end_pos": 203, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "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": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" }, { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ESQPCTSTLPREVGGGHGCT", "down_seq": "PPFPQEARAEISERSGRSPQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "site_lbl": "Ser203" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q6ZN17-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6ZN17-1.221.221", "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": "Q6ZN17-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "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": "Q6ZN17-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17", "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": "GHGCTSPPFPQEARAEISER", "down_seq": "GRSPQEASSTKSSIAPEEQS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser218" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6ZN17-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6ZN17-1.221.221", "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": "Q6ZN17-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "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": "Q6ZN17-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17", "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": "CTSPPFPQEARAEISERSGR", "down_seq": "PQEASSTKSSIAPEEQSKKG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser221" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q6ZN17-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6ZN17-1.218.218", "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": "Q6ZN17-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The KRAS/Lin28B axis maintains stemness of pancreatic cancer cells via the let-7i/TET3 pathway.", "journal": "Molecular oncology", "date": "2021-01", "authors": "Liu Yawen, Wang Dawei, Zhou Meng, Chen Hui, Wang Huizhi, Min Jingyu, Chen Jiaxi, Wu Shuhui, Ni Xiufan, Zhang Youli, Gong Aihua, Xu Min", "evidence": [ { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "reference": [ { "type": "PubMed", "id": "33107691", "url": "https://glygen.org/publication/PubMed/33107691" } ] } ], "crossref": [ { "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33107691", "url": "https://glygen.org/publication/PubMed/33107691", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QEASSTKSSIAPEEQSKKGP", "down_seq": "VQKRKKT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" }, { "database": "PubMed", "id": "33107691", "url": "https://glygen.org/publication/PubMed/33107691" } ], "site_lbl": "Ser243" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q6ZN17-1.245.245", "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": "Q6ZN17-1.54.54", "start_pos": 54, "end_pos": 54, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "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": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" }, { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CKWFNVRMGFGFISMINREG", "down_seq": "PLDIPVDVFVHQSKLFMEGF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "site_lbl": "Ser54" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "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": "Q6ZN17-1.96.96", "start_pos": 96, "end_pos": 96, "uniprot_canonical_ac": "Q6ZN17-1", "length": 250, "uniprot_id": "LN28B_HUMAN", "protein_name": "Protein lin-28 homolog B", "refseq_ac": "NP_001004317", "refseq_name": "protein lin-28 homolog B isoform 1", "gene_name": "LIN28B", "gene_names_uniprotkb": "LIN28B; CSDD2", "gene_names_refseq": "CSDD2; LIN28B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" } ], "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": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" }, { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLKEGEPVEFTFKKSSKGLE", "down_seq": "IRVTGPGGSPCLGSERRPKG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZN17", "url": "https://www.uniprot.org/uniprotkb/Q6ZN17" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q6ZN17", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZN17" } ], "site_lbl": "Ser96" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "245", "end_pos": "245" }, { "start_pos": "3", "end_pos": "3" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "96", "end_pos": "96" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q6ZN17-1.105.105", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6ZN17-1.110.110", "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": "O14662-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "O14662-1", "length": 325, "uniprot_id": "STX16_HUMAN", "protein_name": "Syntaxin-16", "refseq_ac": "NP_001001433", "refseq_name": "syntaxin-16 isoform a", "gene_name": "STX16", "gene_names_uniprotkb": "STX16", "gene_names_refseq": "STX16; SYN-16; SYN16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "O14662", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O14662" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O14662", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O14662", "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": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "O14662", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O14662" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "179", "end_pos": "179" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "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": "O14662-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "O14662-1", "length": 325, "uniprot_id": "STX16_HUMAN", "protein_name": "Syntaxin-16", "refseq_ac": "NP_001001433", "refseq_name": "syntaxin-16 isoform a", "gene_name": "STX16", "gene_names_uniprotkb": "STX16", "gene_names_refseq": "STX16; SYN-16; SYN16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O14662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14662", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GNVVASLAQALQELSTSFRH", "down_seq": "QSGYLKRMKNREERSQHFFD", "snv": [ { "evidence": [ { "id": "O14662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14662" } ], "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": "20", "chr_pos": "58669432", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A179", "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": "snv", "site_list": [ { "start_pos": "179", "end_pos": "179" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "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": "O14662-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "O14662-1", "length": 325, "uniprot_id": "STX16_HUMAN", "protein_name": "Syntaxin-16", "refseq_ac": "NP_001001433", "refseq_name": "syntaxin-16 isoform a", "gene_name": "STX16", "gene_names_uniprotkb": "STX16", "gene_names_refseq": "STX16; SYN-16; SYN16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O14662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14662", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DQLVLVEQNTLMVEEREREI", "down_seq": "QIVQSISDLNEIFRDLGAMI", "snv": [ { "evidence": [ { "id": "O14662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14662" } ], "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": "20", "chr_pos": "58671227", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R241", "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: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": "179", "end_pos": "179" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "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": "O14662-1.325.325", "start_pos": 325, "end_pos": 325, "uniprot_canonical_ac": "O14662-1", "length": 325, "uniprot_id": "STX16_HUMAN", "protein_name": "Syntaxin-16", "refseq_ac": "NP_001001433", "refseq_name": "syntaxin-16 isoform a", "gene_name": "STX16", "gene_names_uniprotkb": "STX16", "gene_names_refseq": "STX16; SYN-16; SYN16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O14662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14662", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ILILFVIIIVLIVVLVGVKS", "down_seq": "", "snv": [ { "evidence": [ { "id": "O14662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14662" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "58676287", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R325", "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: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": "179", "end_pos": "179" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "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": "O14662-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "O14662-1", "length": 325, "uniprot_id": "STX16_HUMAN", "protein_name": "Syntaxin-16", "refseq_ac": "NP_001001433", "refseq_name": "syntaxin-16 isoform a", "gene_name": "STX16", "gene_names_uniprotkb": "STX16", "gene_names_refseq": "STX16; SYN-16; SYN16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O14662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14662", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VSSHITSSPLHSRSIAAELD", "down_seq": "LADDRMALVSGISLDPEAAI", "snv": [ { "evidence": [ { "id": "O14662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14662" } ], "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": "20", "chr_pos": "58659632", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E48", "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": "179", "end_pos": "179" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O14662-1.34.34", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "O14662-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O14662-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O14662-1.53.53", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "O14662-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "O14662-1", "length": 325, "uniprot_id": "STX16_HUMAN", "protein_name": "Syntaxin-16", "refseq_ac": "NP_001001433", "refseq_name": "syntaxin-16 isoform a", "gene_name": "STX16", "gene_names_uniprotkb": "STX16", "gene_names_refseq": "STX16; SYN-16; SYN16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O14662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14662", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TSSPLHSRSIAAELDELADD", "down_seq": "MALVSGISLDPEAAIGVTKR", "snv": [ { "evidence": [ { "id": "O14662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14662" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "58667503", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R53", "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: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: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": "179", "end_pos": "179" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O14662-1.34.34", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "O14662-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "O14662-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O14662-1.48.48", "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": "O14662-1.34.34", "start_pos": 34, "end_pos": 34, "uniprot_canonical_ac": "O14662-1", "length": 325, "uniprot_id": "STX16_HUMAN", "protein_name": "Syntaxin-16", "refseq_ac": "NP_001001433", "refseq_name": "syntaxin-16 isoform a", "gene_name": "STX16", "gene_names_uniprotkb": "STX16", "gene_names_refseq": "STX16; SYN-16; SYN16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662" } ], "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": "O14662-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O14662-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O14662", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O14662", "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": "RNNSIQNRQLLAEQVSSHIT", "down_seq": "SPLHSRSIAAELDELADDRM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O14662", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O14662" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser34" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "179", "end_pos": "179" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "O14662-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O14662-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O14662-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O14662-1.53.53", "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": "O14662-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "O14662-1", "length": 325, "uniprot_id": "STX16_HUMAN", "protein_name": "Syntaxin-16", "refseq_ac": "NP_001001433", "refseq_name": "syntaxin-16 isoform a", "gene_name": "STX16", "gene_names_uniprotkb": "STX16", "gene_names_refseq": "STX16; SYN-16; SYN16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662" } ], "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": "O14662-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O14662-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O14662", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O14662", "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": "NNSIQNRQLLAEQVSSHITS", "down_seq": "PLHSRSIAAELDELADDRMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O14662", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O14662" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser35" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "179", "end_pos": "179" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O14662-1.34.34", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O14662-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O14662-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O14662-1.53.53", "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": "O14662-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "O14662-1", "length": 325, "uniprot_id": "STX16_HUMAN", "protein_name": "Syntaxin-16", "refseq_ac": "NP_001001433", "refseq_name": "syntaxin-16 isoform a", "gene_name": "STX16", "gene_names_uniprotkb": "STX16", "gene_names_refseq": "STX16; SYN-16; SYN16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "TiO(2)-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment.", "journal": "Journal of proteome research", "date": "2008", "authors": "Thingholm TE, Larsen MR, Ingrell CR, Kassem M, Jensen ON", "evidence": [ { "database": "iPTMnet", "id": "O14662-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O14662-1" } ], "reference": [ { "type": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" } ] }, { "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": "O14662-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O14662-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "O14662", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O14662", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522", "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": "RQLLAEQVSSHITSSPLHSR", "down_seq": "IAAELDELADDRMALVSGIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O14662", "url": "https://www.uniprot.org/uniprotkb/O14662" }, { "database": "iPTMnet", "id": "O14662", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O14662" }, { "database": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser41" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "179", "end_pos": "179" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O14662-1.34.34", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O14662-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O14662-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O14662-1.53.53", "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": "Q8N653-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for LZTR1 recognition of RAS GTPases for degradation.", "journal": "Science (New York, N.Y.)", "date": "2025-09-11", "authors": "Dharmaiah Srisathiyanarayanan, Bonsor Daniel A, Mo Stephanie P, Fernandez-Cabrera Alvaro, Chan Albert H, Messing Simon, Drew Matthew, Vega Martha, Nissley Dwight V, Esposito Dominic, Castel Pau, Simanshu Dhirendra K", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "reference": [ { "type": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "crossref": [ { "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DVKDCSWCRAFTTGTPPAPR", "down_seq": "HHSAVVYGSSMFVFGGYTGD", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Abolishes interaction with RIT1.", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" }, { "database": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8N653-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8N653-1.118.118", "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": "Q8N653-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for LZTR1 recognition of RAS GTPases for degradation.", "journal": "Science (New York, N.Y.)", "date": "2025-09-11", "authors": "Dharmaiah Srisathiyanarayanan, Bonsor Daniel A, Mo Stephanie P, Fernandez-Cabrera Alvaro, Chan Albert H, Messing Simon, Drew Matthew, Vega Martha, Nissley Dwight V, Esposito Dominic, Castel Pau, Simanshu Dhirendra K", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "reference": [ { "type": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "crossref": [ { "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "AVVYGSSMFVFGGYTGDIYS", "down_seq": "SNLKNKNDLFEYKFATGQWT", "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "Abolishes interaction with RIT1.", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" }, { "database": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "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": "Q8N653-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Dominant Noonan syndrome-causing LZTR1 mutations specifically affect the Kelch domain substrate-recognition surface and enhance RAS-MAPK signaling.", "journal": "Human molecular genetics", "date": "2019", "authors": "Motta M, Fidan M, Bellacchio E, Pantaleoni F, Schneider-Heieck K, Coppola S, Borck G, Salviati L, Zenker M, Cirstea IC, Tartaglia M", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "reference": [ { "type": "PubMed", "id": "30481304", "url": "https://glygen.org/publication/PubMed/30481304" } ] } ], "crossref": [ { "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30481304", "url": "https://glygen.org/publication/PubMed/30481304", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VARSAHGATVYSDKLWIFAG", "down_seq": "DGNARLNDMWTIGLQDRELT", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "H", "comment": "Increased RAS-MAPK signaling.", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" }, { "database": "PubMed", "id": "30481304", "url": "https://glygen.org/publication/PubMed/30481304" } ] }, { "sequence_org": "Y", "sequence_mut": "N", "comment": "Increased RAS-MAPK signaling.", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" }, { "database": "PubMed", "id": "30481304", "url": "https://glygen.org/publication/PubMed/30481304" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8N653-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8N653-1.195.195", "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": "Q8N653-1.230.230", "start_pos": 230, "end_pos": 230, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for LZTR1 recognition of RAS GTPases for degradation.", "journal": "Science (New York, N.Y.)", "date": "2025-09-11", "authors": "Dharmaiah Srisathiyanarayanan, Bonsor Daniel A, Mo Stephanie P, Fernandez-Cabrera Alvaro, Chan Albert H, Messing Simon, Drew Matthew, Vega Martha, Nissley Dwight V, Esposito Dominic, Castel Pau, Simanshu Dhirendra K", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "reference": [ { "type": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "crossref": [ { "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RELTCWEEVAQSGEIPPSCC", "down_seq": "FPVAVCRDKMFVFSGQSGAK", "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "Abolishes interaction with RIT1.", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" }, { "database": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q8N653-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8N653-1.248.248", "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": "Q8N653-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for LZTR1 recognition of RAS GTPases for degradation.", "journal": "Science (New York, N.Y.)", "date": "2025-09-11", "authors": "Dharmaiah Srisathiyanarayanan, Bonsor Daniel A, Mo Stephanie P, Fernandez-Cabrera Alvaro, Chan Albert H, Messing Simon, Drew Matthew, Vega Martha, Nissley Dwight V, Esposito Dominic, Castel Pau, Simanshu Dhirendra K", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "reference": [ { "type": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "crossref": [ { "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KDKTWTRIPTEHLLRGSPPP", "down_seq": "QRRYGHTMVAFDRHLYVFGG", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "L", "comment": "Abolishes interaction with RIT1.", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" }, { "database": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20991678", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P281", "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: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: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" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8N653-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8N653-1.283.283", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8N653-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8N653-1.286.286", "categories": [ "snv_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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8N653-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for LZTR1 recognition of RAS GTPases for degradation.", "journal": "Science (New York, N.Y.)", "date": "2025-09-11", "authors": "Dharmaiah Srisathiyanarayanan, Bonsor Daniel A, Mo Stephanie P, Fernandez-Cabrera Alvaro, Chan Albert H, Messing Simon, Drew Matthew, Vega Martha, Nissley Dwight V, Esposito Dominic, Castel Pau, Simanshu Dhirendra K", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "reference": [ { "type": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "crossref": [ { "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KTWTRIPTEHLLRGSPPPPQ", "down_seq": "RYGHTMVAFDRHLYVFGGAA", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Abolishes interaction with RIT1.", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" }, { "database": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8N653-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8N653-1.281.281", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8N653-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8N653-1.286.286", "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": "Q8N653-1.412.412", "start_pos": 412, "end_pos": 412, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural basis for LZTR1 recognition of RAS GTPases for degradation.", "journal": "Science (New York, N.Y.)", "date": "2025-09-11", "authors": "Dharmaiah Srisathiyanarayanan, Bonsor Daniel A, Mo Stephanie P, Fernandez-Cabrera Alvaro, Chan Albert H, Messing Simon, Drew Matthew, Vega Martha, Nissley Dwight V, Esposito Dominic, Castel Pau, Simanshu Dhirendra K", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "reference": [ { "type": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "crossref": [ { "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AAAVISDAMYIFGGTVDNNI", "down_seq": "SGEMYRFQFSCYPKCTLHED", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "C", "comment": "Abolishes interaction with RIT1.", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" }, { "database": "PubMed", "id": "40934300", "url": "https://glygen.org/publication/PubMed/40934300" } ] } ], "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "22", "chr_pos": "20992878", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R412", "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" } ] }, { "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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8N653-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8N653-1.404.404", "categories": [ "snv_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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8N653-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Dominant Noonan syndrome-causing LZTR1 mutations specifically affect the Kelch domain substrate-recognition surface and enhance RAS-MAPK signaling.", "journal": "Human molecular genetics", "date": "2019", "authors": "Motta M, Fidan M, Bellacchio E, Pantaleoni F, Schneider-Heieck K, Coppola S, Borck G, Salviati L, Zenker M, Cirstea IC, Tartaglia M", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "reference": [ { "type": "PubMed", "id": "30481304", "url": "https://glygen.org/publication/PubMed/30481304" } ] } ], "crossref": [ { "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30481304", "url": "https://glygen.org/publication/PubMed/30481304", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "HTVVAYKDAIYVFGGDNGKT", "down_seq": "LNDLLRFDVKDCSWCRAFTT", "mutagenesis": [ { "sequence_org": "M", "sequence_mut": "V", "comment": "Increased RAS-MAPK signaling.", "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" }, { "database": "PubMed", "id": "30481304", "url": "https://glygen.org/publication/PubMed/30481304" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8N653-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8N653-1.104.104", "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": "Q8N653-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GGDNGKTMLNDLLRFDVKDC", "down_seq": "WCRAFTTGTPPAPRYHHSAV", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "606", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20985888", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S104", "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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8N653-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8N653-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8N653-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8N653-1.119.119", "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": "Q8N653-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FDVKDCSWCRAFTTGTPPAP", "down_seq": "YHHSAVVYGSSMFVFGGYTG", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "22", "chr_pos": "20987536", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R118", "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: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" } ] }, { "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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8N653-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8N653-1.119.119", "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": "Q8N653-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EWKIEGRLPVARSAHGATVY", "down_seq": "DKLWIFAGYDGNARLNDMWT", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20988830", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S184", "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: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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q8N653-1.193.193", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8N653-1.195.195", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8N653-1.195.195", "start_pos": 195, "end_pos": 195, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "RSAHGATVYSDKLWIFAGYD", "down_seq": "NARLNDMWTIGLQDRELTCW", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20988862", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G195", "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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8N653-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8N653-1.193.193", "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": "Q8N653-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "EIPPSCCNFPVAVCRDKMFV", "down_seq": "SGQSGAKITNNLFQFEFKDK", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20990463", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "F243", "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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8N653-1.230.230", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8N653-1.248.248", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8N653-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "CCNFPVAVCRDKMFVFSGQS", "down_seq": "AKITNNLFQFEFKDKTWTRI", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "22", "chr_pos": "20990476", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G248", "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: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: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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8N653-1.230.230", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8N653-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8N653-1.267.267", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8N653-1.267.267", "start_pos": 267, "end_pos": 267, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SGAKITNNLFQFEFKDKTWT", "down_seq": "IPTEHLLRGSPPPPQRRYGH", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "4", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "22", "chr_pos": "20991636", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R267", "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: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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8N653-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8N653-1.281.281", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8N653-1.283.283", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8N653-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8N653-1.286.286", "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": "Q8N653-1.284.284", "start_pos": 284, "end_pos": 284, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TWTRIPTEHLLRGSPPPPQR", "down_seq": "YGHTMVAFDRHLYVFGGAAD", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "22", "chr_pos": "20991687", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R284", "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: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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8N653-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8N653-1.281.281", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8N653-1.283.283", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8N653-1.286.286", "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": "Q8N653-1.286.286", "start_pos": 286, "end_pos": 286, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TRIPTEHLLRGSPPPPQRRY", "down_seq": "HTMVAFDRHLYVFGGAADNT", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20991692", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G286", "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: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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8N653-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8N653-1.281.281", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8N653-1.283.283", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8N653-1.284.284", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8N653-1.392.392", "start_pos": 392, "end_pos": 392, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TSAKQPTQPASELPSGRLFH", "down_seq": "AAVISDAMYIFGGTVDNNIR", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "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": "22", "chr_pos": "20992819", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A392", "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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q8N653-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8N653-1.412.412", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8N653-1.404.404", "start_pos": 404, "end_pos": 404, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LPSGRLFHAAAVISDAMYIF", "down_seq": "GTVDNNIRSGEMYRFQFSCY", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "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": "22", "chr_pos": "20992854", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G404", "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" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8N653-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8N653-1.412.412", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8N653-1.440.440", "start_pos": 440, "end_pos": 440, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QFSCYPKCTLHEDYGRLWES", "down_seq": "QFCDVEFVLGEKEECVQGHV", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "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": "22", "chr_pos": "20993720", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R440", "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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "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": "Q8N653-1.466.466", "start_pos": 466, "end_pos": 466, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EFVLGEKEECVQGHVAIVTA", "down_seq": "SRWLRRKITQARERLAQKLE", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20993967", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R466", "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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "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": "Q8N653-1.528.528", "start_pos": 528, "end_pos": 528, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LLHVAIREAEARPFEVLMQF", "down_seq": "YTDKIKYPRKGHVEDVLLIM", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20994236", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "L528", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "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": "Q8N653-1.664.664", "start_pos": 664, "end_pos": 664, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PVDIGTSLIQDMKAYLEGAG", "down_seq": "EFCDITLLLDGHPRPAHKAI", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20995794", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A664", "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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q8N653-1.675.675", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8N653-1.675.675", "start_pos": 675, "end_pos": 675, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MKAYLEGAGAEFCDITLLLD", "down_seq": "HPRPAHKAILAARSSYFEAM", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "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 (5).", "chr_id": "22", "chr_pos": "20995826", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G675", "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" } ] }, { "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: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": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8N653-1.664.664", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8N653-1.700.700", "start_pos": 700, "end_pos": 700, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "AHKAILAARSSYFEAMFRSF", "down_seq": "PEDGQVNISIGEMVPSRQAF", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20995993", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "M700", "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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8N653-1.702.702", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8N653-1.716.716", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8N653-1.702.702", "start_pos": 702, "end_pos": 702, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KAILAARSSYFEAMFRSFMP", "down_seq": "DGQVNISIGEMVPSRQAFES", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "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": "22", "chr_pos": "20995997", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E702", "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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8N653-1.700.700", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8N653-1.716.716", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8N653-1.716.716", "start_pos": 716, "end_pos": 716, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FRSFMPEDGQVNISIGEMVP", "down_seq": "RQAFESMLRYIYYGEVNMPP", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "22", "chr_pos": "20996041", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S716", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8N653-1.700.700", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8N653-1.702.702", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8N653-1.755.755", "start_pos": 755, "end_pos": 755, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PPEDSLYLFAAPYYYGFYNN", "down_seq": "LQAYCKQNLEMNVTVQNVLQ", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20996739", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R755", "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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "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": "Q8N653-1.810.810", "start_pos": 810, "end_pos": 810, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RHCLHIIVHQFTKVSKLPTL", "down_seq": "SLSQQLLLDIIDSLASHISD", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20997253", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R810", "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: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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "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": "Q8N653-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "Q8N653-1", "length": 840, "uniprot_id": "LZTR1_HUMAN", "protein_name": "Leucine-zipper-like transcriptional regulator 1", "refseq_ac": "NP_006758", "refseq_name": "leucine-zipper-like transcriptional regulator 1", "gene_name": "LZTR1", "gene_names_uniprotkb": "LZTR1; TCFL2", "gene_names_refseq": "BTBD29; LZTR-1; LZTR1; NS10; NS2; SWNTS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N653", "url": "https://www.uniprot.org/uniprotkb/Q8N653" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N653", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KDAIYVFGGDNGKTMLNDLL", "down_seq": "FDVKDCSWCRAFTTGTPPAP", "snv": [ { "evidence": [ { "id": "Q8N653", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N653" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "22", "chr_pos": "20985866", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R97", "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" } ] }, { "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": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "664", "end_pos": "664" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "755", "end_pos": "755" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "97", "end_pos": "97" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8N653-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8N653-1.104.104", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8WXG6-1.1485.1485", "start_pos": 1485, "end_pos": 1485, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "rs753230694", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753230694", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753230694", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753230694", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753230694", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753230694", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VVLRSNIGTVYERWWYEKLI", "down_seq": "MTYCPKTKVLCLWRRNGSET", "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": "LINMTYCPKTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1485", "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" } ] } ], "snv": [ { "evidence": [ { "id": "rs753230694", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753230694" }, { "id": "rs753230694", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753230694" }, { "id": "rs753230694", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753230694" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NMT->SMT).", "chr_id": "11", "chr_pos": "47323747", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1485", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.1487.1487", "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": 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": "Q8WXG6-1.1487.1487", "start_pos": 1487, "end_pos": 1487, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "OGA mutant aberrantly hydrolyzes O-GlcNAc modification from PDLIM7 to modulate p53 and cytoskeleton in promoting cancer cell malignancy.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-06-11", "authors": "Hu Chia-Wei, Wang Ao, Fan Dacheng, Worth Matthew, Chen Zhengwei, Huang Junfeng, Xie Jinshan, Macdonald John, Li Lingjun, Jiang Jiaoyang", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q8WXG6", "url": "https://oglcnac.org/atlas/detail/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015" } ] } ], "crossref": [ { "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "https://oglcnac.org/atlas/detail/Q8WXG6", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs371408187", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371408187", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371408187", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371408187", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371408187", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371408187", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LRSNIGTVYERWWYEKLINM", "down_seq": "YCPKTKVLCLWRRNGSETQL", "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": "Thr1487", "evidence": [ { "id": "38838015", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38838015" }, { "id": "Q8WXG6", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8WXG6" } ] } ], "snv": [ { "evidence": [ { "id": "rs371408187", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371408187" }, { "id": "rs371408187", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371408187" }, { "id": "rs371408187", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371408187" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NMT->NMI); o-glyco-site-loss (T->I).", "chr_id": "11", "chr_pos": "47323753", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1487", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.1485.1485", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q8WXG6-1.826.826", "start_pos": 826, "end_pos": 826, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q8WXG6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WXG6" }, { "database": "O-GlcNAc Atlas", "id": "Q8WXG6", "url": "https://oglcnac.org/atlas/detail/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "Q8WXG6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "Q8WXG6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WXG6", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "https://oglcnac.org/atlas/detail/Q8WXG6", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2059985041", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2059985041", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2059985041", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2059985041#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QKLLRPNSLRLASDSDAESD", "down_seq": "RASSPNSTVSNTSTEGFGGI", "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": "Ser826", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "Q8WXG6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WXG6" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "Q8WXG6", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8WXG6" } ] } ], "snv": [ { "evidence": [ { "id": "rs2059985041", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2059985041" }, { "id": "rs2059985041", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2059985041#frequency_tab" } ], "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": "11", "chr_pos": "47285516", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S826", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8WXG6-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.818.818", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WXG6-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.834.834", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8WXG6-1.834.834", "start_pos": 834, "end_pos": 834, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q8WXG6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WXG6" }, { "database": "O-GlcNAc Atlas", "id": "Q8WXG6", "url": "https://oglcnac.org/atlas/detail/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "Q8WXG6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "Q8WXG6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q8WXG6", "url": "https://oglcnac.org/atlas/detail/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WXG6", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "https://oglcnac.org/atlas/detail/Q8WXG6", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LRLASDSDAESDSRASSPNS", "down_seq": "VSNTSTEGFGGIMSFASSLY", "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": "Thr834", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "Q8WXG6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WXG6" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "Q8WXG6", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8WXG6" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8WXG6-1.818.818", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WXG6-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.826.826", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WXG6-1.848.848", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8WXG6-1.856.856", "start_pos": 856, "end_pos": 856, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "rs140000041", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140000041", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SNTSTEGFGGIMSFASSLYR", "down_seq": "HSTSFSLSNLTLPTKGAREK", "glycosylation": [ { "glytoucan_ac": "G59324HL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NHSTSFSLSNLTLPTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn856", "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" } ] } ], "snv": [ { "evidence": [ { "id": "rs140000041", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140000041" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NHS->SHS).", "chr_id": "11", "chr_pos": "47286448", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N856", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.848.848", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.858.858", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WXG6-1.862.862", "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": 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": "Q8WXG6-1.500.500", "start_pos": 500, "end_pos": 500, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs770084863", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770084863", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770084863", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770084863", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770084863", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770084863#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs770084863", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770084863", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs770084863", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs770084863", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NDVDSVDVATRVAMVRFFNS", "down_seq": "NVLQGFQMHTRTLRLFPRPV", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" }, { "id": "rs770084863", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770084863" }, { "id": "rs770084863", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770084863" }, { "id": "rs770084863", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770084863#frequency_tab" }, { "id": "rs770084863", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770084863" }, { "id": "rs770084863", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs770084863" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); n-glyco-sequon-gain (NSA->NST).", "chr_id": "11", "chr_pos": "47282409", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A500", "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", "ebi" ] }, { "evidence": [ { "id": "rs770084863", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770084863" }, { "id": "rs770084863", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770084863" }, { "id": "rs770084863", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770084863#frequency_tab" }, { "id": "rs770084863", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770084863" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSA->NSS).", "chr_id": "11", "chr_pos": "47282409", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A500", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": 1 } ], "sort_fields": [ "subjects_tested", "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": "Q8WXG6-1.858.858", "start_pos": 858, "end_pos": 858, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "rs757555336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757555336", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757555336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757555336", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757555336", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757555336", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1225053518", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225053518", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1225053518", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225053518", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "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": "TSTEGFGGIMSFASSLYRNH", "down_seq": "TSFSLSNLTLPTKGAREKAT", "snv": [ { "evidence": [ { "id": "rs757555336", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757555336" }, { "id": "rs757555336", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757555336" }, { "id": "rs757555336", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757555336" } ], "glycoeffect": [ "n-glyco-sequon-gain", "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (STS->NTS); n-glyco-sequon-loss (NHS->NHN).", "chr_id": "11", "chr_pos": "47286454", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S858", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1225053518", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225053518" }, { "id": "rs1225053518", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225053518" } ], "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 (NHS->NHG).", "chr_id": "11", "chr_pos": "47286453", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S858", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser858" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8WXG6-1.848.848", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.856.856", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WXG6-1.862.862", "categories": [ "phosphorylation_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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "Q8WXG6-1.1067.1067", "start_pos": 1067, "end_pos": 1067, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765957900", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765957900", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765957900", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765957900", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765957900", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765957900", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "HYYSKEPDKRKRSPTESVNT", "down_seq": "VGKDPGLAGRGDPKAMAQLR", "snv": [ { "evidence": [ { "id": "rs765957900", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765957900" }, { "id": "rs765957900", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765957900" }, { "id": "rs765957900", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765957900" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTP->NTS).", "chr_id": "11", "chr_pos": "47290654", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1067", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.1059.1059", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WXG6-1.1061.1061", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WXG6-1.1066.1066", "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": "Q8WXG6-1.1161.1161", "start_pos": 1161, "end_pos": 1161, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EVIKPVFDLGETEEKKSQIS", "down_seq": "DSGVSLTSSSQRTDQDSVIG", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "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": "11", "chr_pos": "47293948", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A1161", "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: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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q8WXG6-1.1166.1166", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.1169.1169", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WXG6-1.1174.1174", "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": "Q8WXG6-1.1166.1166", "start_pos": 1166, "end_pos": 1166, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs375878509", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375878509", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs375878509", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375878509", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs375878509", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375878509#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs375878509", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375878509", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs375878509", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs375878509", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VFDLGETEEKKSQISADSGV", "down_seq": "LTSSSQRTDQDSVIGVSPAV", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" }, { "id": "rs375878509", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375878509" }, { "id": "rs375878509", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375878509" }, { "id": "rs375878509", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375878509#frequency_tab" }, { "id": "rs375878509", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375878509" }, { "id": "rs375878509", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs375878509" } ], "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 (SLT->NLT).", "chr_id": "11", "chr_pos": "47293964", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1166", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8WXG6-1.1161.1161", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WXG6-1.1169.1169", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.1174.1174", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WXG6-1.1183.1183", "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": "Q8WXG6-1.1169.1169", "start_pos": 1169, "end_pos": 1169, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2071231803", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2071231803", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2071231803", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2071231803", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGETEEKKSQISADSGVSLT", "down_seq": "SSQRTDQDSVIGVSPAVMIR", "snv": [ { "evidence": [ { "id": "rs2071231803", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2071231803" }, { "id": "rs2071231803", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2071231803" } ], "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": "11", "chr_pos": "47295943", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1169", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.1161.1161", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8WXG6-1.1166.1166", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WXG6-1.1174.1174", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WXG6-1.1183.1183", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WXG6-1.1189.1189", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WXG6-1.1189.1189", "start_pos": 1189, "end_pos": 1189, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SSSQRTDQDSVIGVSPAVMI", "down_seq": "SSSQDSEVSTVVSNSSGETL", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "47295545", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1189", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WXG6-1.1169.1169", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WXG6-1.1174.1174", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WXG6-1.1183.1183", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WXG6-1.1190.1190", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WXG6-1.1199.1199", "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": "Q8WXG6-1.1190.1190", "start_pos": 1190, "end_pos": 1190, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1207239297", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1207239297", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1207239297", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1207239297#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1207239297", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1207239297", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1265998590", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265998590", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1265998590", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1265998590#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1265998590", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1265998590", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs946652400", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs946652400", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs946652400", "url": "https://www.ncbi.nlm.nih.gov/snp/rs946652400#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSQRTDQDSVIGVSPAVMIR", "down_seq": "SSQDSEVSTVVSNSSGETLG", "snv": [ { "evidence": [ { "id": "rs1207239297", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1207239297" }, { "id": "rs1207239297", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1207239297#frequency_tab" }, { "id": "rs1207239297", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1207239297" }, { "id": "rs1265998590", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265998590" }, { "id": "rs1265998590", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1265998590#frequency_tab" }, { "id": "rs1265998590", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1265998590" }, { "id": "rs946652400", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs946652400" }, { "id": "rs946652400", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs946652400#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 (SSS->NSS).", "chr_id": "11", "chr_pos": "47295979", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1190", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8WXG6-1.1174.1174", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WXG6-1.1183.1183", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WXG6-1.1189.1189", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WXG6-1.1199.1199", "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": "Q8WXG6-1.1220.1220", "start_pos": 1220, "end_pos": 1220, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2071245823", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2071245823", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2071245823", "url": "https://www.ensembl.org/id/rs2071245823", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VVSNSSGETLGADSDLSSNA", "down_seq": "DGPGGEGSVHLASSRGTLSD", "snv": [ { "evidence": [ { "id": "rs2071245823", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2071245823" }, { "id": "rs2071245823", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2071245823" } ], "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": "11", "chr_pos": "47295954", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1220", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8WXG6-1.1226.1226", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WXG6-1.1237.1237", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8WXG6-1.1239.1239", "categories": [ "snv_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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WXG6-1.1226.1226", "start_pos": 1226, "end_pos": 1226, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GETLGADSDLSSNAGDGPGG", "down_seq": "GSVHLASSRGTLSDSEIETN", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "47295972", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E1226", "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: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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8WXG6-1.1220.1220", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WXG6-1.1237.1237", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WXG6-1.1239.1239", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WXG6-1.1241.1241", "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": "Q8WXG6-1.1239.1239", "start_pos": 1239, "end_pos": 1239, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "title": "Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer.", "journal": "Analytical chemistry", "date": "2010", "authors": "Raijmakers R, Kraiczek K, de Jong AP, Mohammed S, Heck AJ", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] } ], "crossref": [ { "id": "rs868563468", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868563468", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs868563468", "url": "https://www.ncbi.nlm.nih.gov/snp/rs868563468#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs868563468", "url": "http://gnomad.broadinstitute.org/awesome?query=rs868563468", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs868563468", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs868563468", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AGDGPGGEGSVHLASSRGTL", "down_seq": "DSEIETNSATSTIFGKAHSL", "snv": [ { "evidence": [ { "id": "rs868563468", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868563468" }, { "id": "rs868563468", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs868563468#frequency_tab" }, { "id": "rs868563468", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs868563468" }, { "id": "rs868563468", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs868563468" } ], "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 (SDS->NDS).", "chr_id": "11", "chr_pos": "47309281", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1239", "keywords": [ "ebi", "somatic" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ], "site_lbl": "Ser1239" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8WXG6-1.1220.1220", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WXG6-1.1226.1226", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.1237.1237", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.1241.1241", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WXG6-1.1248.1248", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q8WXG6-1.1248.1248", "start_pos": 1248, "end_pos": 1248, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2071324405", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2071324405", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2071324405", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2071324405#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SVHLASSRGTLSDSEIETNS", "down_seq": "TSTIFGKAHSLKPSIKEKLA", "snv": [ { "evidence": [ { "id": "rs2071324405", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2071324405" }, { "id": "rs2071324405", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2071324405#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSA->NSS).", "chr_id": "11", "chr_pos": "47296038", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1248", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8WXG6-1.1237.1237", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WXG6-1.1239.1239", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WXG6-1.1241.1241", "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": "Q8WXG6-1.1369.1369", "start_pos": 1369, "end_pos": 1369, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IDRYLSLGEHDRKRLEDDED", "down_seq": "LLATLLHNLISYMLLMKVNK", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "47309559", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1369", "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: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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758838278", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758838278", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758838278", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758838278", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758838278", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758838278", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs758838278", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs758838278", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRGKEGTHATCASEEGGTES", "down_seq": "ESGSSLQPLSADSTPDVNQS", "snv": [ { "evidence": [ { "id": "rs758838278", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758838278" }, { "id": "rs758838278", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758838278" }, { "id": "rs758838278", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758838278" }, { "id": "rs758838278", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs758838278" } ], "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 (SES->NES).", "chr_id": "11", "chr_pos": "47275111", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S136", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WXG6-1.156.156", "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": "Q8WXG6-1.138.138", "start_pos": 138, "end_pos": 138, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs755698073", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755698073", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755698073", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755698073", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755698073", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755698073#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs755698073", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755698073", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GKEGTHATCASEEGGTESSE", "down_seq": "GSSLQPLSADSTPDVNQSPR", "snv": [ { "evidence": [ { "id": "rs755698073", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755698073" }, { "id": "rs755698073", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755698073" }, { "id": "rs755698073", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755698073#frequency_tab" }, { "id": "rs755698073", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755698073" } ], "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": "11", "chr_pos": "47274913", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S138", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WXG6-1.156.156", "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": "Q8WXG6-1.1390.1390", "start_pos": 1390, "end_pos": 1390, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs372333972", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372333972", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372333972", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372333972", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372333972", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372333972#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372333972", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372333972", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LLATLLHNLISYMLLMKVNK", "down_seq": "DIRKKVRRLMGKSHIGLVYS", "snv": [ { "evidence": [ { "id": "rs372333972", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372333972" }, { "id": "rs372333972", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372333972" }, { "id": "rs372333972", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372333972#frequency_tab" }, { "id": "rs372333972", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372333972" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKN->NKS).", "chr_id": "11", "chr_pos": "47311814", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1390", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.1398.1398", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WXG6-1.1398.1398", "start_pos": 1398, "end_pos": 1398, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LISYMLLMKVNKNDIRKKVR", "down_seq": "LMGKSHIGLVYSQQINEVLD", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "47311765", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1398", "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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.1390.1390", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8WXG6-1.1424.1424", "start_pos": 1424, "end_pos": 1424, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1052682127", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1052682127", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1052682127", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1052682127#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1052682127", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1052682127", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HIGLVYSQQINEVLDQLANL", "down_seq": "GRDLSIWSSGSRHMKKQTFV", "snv": [ { "evidence": [ { "id": "rs1052682127", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1052682127" }, { "id": "rs1052682127", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1052682127#frequency_tab" }, { "id": "rs1052682127", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1052682127" } ], "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": "11", "chr_pos": "47315221", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1424", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.1426.1426", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8WXG6-1.1427.1427", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WXG6-1.1426.1426", "start_pos": 1426, "end_pos": 1426, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs927975676", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs927975676", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs927975676", "url": "https://www.ncbi.nlm.nih.gov/snp/rs927975676#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs927975676", "url": "http://gnomad.broadinstitute.org/awesome?query=rs927975676", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GLVYSQQINEVLDQLANLNG", "down_seq": "DLSIWSSGSRHMKKQTFVVH", "snv": [ { "evidence": [ { "id": "rs927975676", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs927975676" }, { "id": "rs927975676", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs927975676#frequency_tab" }, { "id": "rs927975676", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs927975676" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGR->NGC).", "chr_id": "11", "chr_pos": "47315226", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1426", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.1424.1424", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WXG6-1.1427.1427", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WXG6-1.1427.1427", "start_pos": 1427, "end_pos": 1427, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773023506", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773023506", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773023506", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773023506", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773023506", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773023506#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773023506", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773023506", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LVYSQQINEVLDQLANLNGR", "down_seq": "LSIWSSGSRHMKKQTFVVHA", "snv": [ { "evidence": [ { "id": "rs773023506", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773023506" }, { "id": "rs773023506", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773023506" }, { "id": "rs773023506", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773023506#frequency_tab" }, { "id": "rs773023506", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773023506" } ], "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": "11", "chr_pos": "47315229", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1427", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8WXG6-1.1424.1424", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8WXG6-1.1426.1426", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WXG6-1.1462.1462", "start_pos": 1462, "end_pos": 1462, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748913496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748913496", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748913496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748913496", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748913496", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748913496#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748913496", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748913496", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TFVVHAGTDTNGDIFFMEVC", "down_seq": "DCVVLRSNIGTVYERWWYEK", "snv": [ { "evidence": [ { "id": "rs748913496", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748913496" }, { "id": "rs748913496", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748913496" }, { "id": "rs748913496", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748913496#frequency_tab" }, { "id": "rs748913496", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748913496" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DDC->NDC).", "chr_id": "11", "chr_pos": "47323677", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1462", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.1516.1516", "start_pos": 1516, "end_pos": 1516, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CLWRRNGSETQLNKFYTKKC", "down_seq": "ELYYCVKDSMERAAARQQSI", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "11", "chr_pos": "47324269", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1516", "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: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: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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q8WXG6-1.1532.1532", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8WXG6-1.1532.1532", "start_pos": 1532, "end_pos": 1532, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TKKCRELYYCVKDSMERAAA", "down_seq": "QQSIKPGPELGGEFPVQDLK", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "11", "chr_pos": "47324317", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1532", "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: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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8WXG6-1.1516.1516", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8WXG6-1.1589.1589", "start_pos": 1589, "end_pos": 1589, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KFMHNQVFIELNHIKKCNTV", "down_seq": "GVFVLEEFVPEIKEVVSHKY", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "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": "11", "chr_pos": "47326780", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1589", "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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.1621.1621", "start_pos": 1621, "end_pos": 1621, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "IKEVVSHKYKTPMAHEICYS", "down_seq": "LCLFSYVAAVHSSEEDLRTP", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "47329067", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V1621", "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: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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779283284", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779283284", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779283284", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779283284", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779283284", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779283284#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779283284", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779283284", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SHYPFFSTFRECLYTLKRLV", "down_seq": "CCSERLLGKKLGIPRGVQRD", "snv": [ { "evidence": [ { "id": "rs779283284", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779283284" }, { "id": "rs779283284", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779283284" }, { "id": "rs779283284", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779283284#frequency_tab" }, { "id": "rs779283284", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779283284" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DCC->NCC).", "chr_id": "11", "chr_pos": "47275101", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D201", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IVGARHPSSDSVAQTPELLR", "down_seq": "YPLEDHTEFPLPPDVVFFCQ", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "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": "11", "chr_pos": "47274609", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R37", "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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q8WXG6-1.42.42", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8WXG6-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2048132612", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2048132612", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2048132612", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2048132612#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HPSSDSVAQTPELLRRYPLE", "down_seq": "HTEFPLPPDVVFFCQPEGCL", "snv": [ { "evidence": [ { "id": "rs2048132612", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2048132612" }, { "id": "rs2048132612", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2048132612#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DHT->NHT).", "chr_id": "11", "chr_pos": "47274624", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D42", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8WXG6-1.37.37", "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": "Q8WXG6-1.434.434", "start_pos": 434, "end_pos": 434, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PILPEPESLELKKHLKQALA", "down_seq": "MSLNTQPILNLEKFHEGQEI", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SMS->NMS).", "chr_id": "11", "chr_pos": "47281585", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S434", "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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.558.558", "start_pos": 558, "end_pos": 558, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758237114", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758237114", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758237114", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758237114", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758237114", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758237114#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs758237114", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758237114", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "FAEKLARTQAVEYFGEWILN", "down_seq": "TNYAFQRIHNNMFDPALIGD", "snv": [ { "evidence": [ { "id": "rs758237114", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758237114" }, { "id": "rs758237114", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758237114" }, { "id": "rs758237114", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758237114#frequency_tab" }, { "id": "rs758237114", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758237114" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPT->NAT).", "chr_id": "11", "chr_pos": "47282583", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P558", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q8WXG6-1.570.570", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WXG6-1.570.570", "start_pos": 570, "end_pos": 570, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs772120601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772120601", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772120601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772120601", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772120601", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772120601#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772120601", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772120601", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "YFGEWILNPTNYAFQRIHNN", "down_seq": "FDPALIGDKPKWYAHQLQPI", "snv": [ { "evidence": [ { "id": "rs772120601", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772120601" }, { "id": "rs772120601", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772120601" }, { "id": "rs772120601", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772120601#frequency_tab" }, { "id": "rs772120601", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772120601" } ], "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": "11", "chr_pos": "47282816", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M570", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8WXG6-1.558.558", "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": "Q8WXG6-1.597.597", "start_pos": 597, "end_pos": 597, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780141097", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780141097", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780141097", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780141097", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780141097", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780141097", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GDKPKWYAHQLQPIHYRVYD", "down_seq": "NSQLAEALSVPPERDSDSEP", "snv": [ { "evidence": [ { "id": "rs780141097", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780141097" }, { "id": "rs780141097", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780141097" }, { "id": "rs780141097", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780141097" } ], "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 (SNS->NNS).", "chr_id": "11", "chr_pos": "47282897", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S597", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.621.621", "start_pos": 621, "end_pos": 621, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2059246302", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2059246302", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2059246302", "url": "https://www.ensembl.org/id/rs2059246302", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAEALSVPPERDSDSEPTDD", "down_seq": "GSDSMDYDDSSSSYSSLGDF", "snv": [ { "evidence": [ { "id": "rs2059246302", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2059246302" }, { "id": "rs2059246302", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2059246302" } ], "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": "11", "chr_pos": "47284474", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S621", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8WXG6-1.624.624", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WXG6-1.630.630", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WXG6-1.624.624", "start_pos": 624, "end_pos": 624, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ALSVPPERDSDSEPTDDSGS", "down_seq": "SMDYDDSSSSYSSLGDFVSE", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "47284185", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D624", "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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8WXG6-1.621.621", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WXG6-1.630.630", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8WXG6-1.630.630", "start_pos": 630, "end_pos": 630, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs558934952", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558934952", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs558934952", "url": "https://www.ncbi.nlm.nih.gov/snp/rs558934952#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs558934952", "url": "http://gnomad.broadinstitute.org/awesome?query=rs558934952", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ERDSDSEPTDDSGSDSMDYD", "down_seq": "SSSSYSSLGDFVSEMMKCDI", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" }, { "id": "rs558934952", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558934952" }, { "id": "rs558934952", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs558934952#frequency_tab" }, { "id": "rs558934952", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs558934952" } ], "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 (DSS->NSS).", "chr_id": "11", "chr_pos": "47284203", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D630", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8WXG6-1.621.621", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WXG6-1.624.624", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8WXG6-1.699.699", "start_pos": 699, "end_pos": 699, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QKEAEEPGPDSENSQENPPL", "down_seq": "SSSSTTASSSPSTVIHGANS", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "11", "chr_pos": "47284503", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R699", "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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8WXG6-1.689.689", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WXG6-1.692.692", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.701.701", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.707.707", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WXG6-1.709.709", "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": "Q8WXG6-1.701.701", "start_pos": 701, "end_pos": 701, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1238676208", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1238676208", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1238676208", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1238676208#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1238676208", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1238676208", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EAEEPGPDSENSQENPPLRS", "down_seq": "SSTTASSSPSTVIHGANSEP", "snv": [ { "evidence": [ { "id": "rs1238676208", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1238676208" }, { "id": "rs1238676208", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1238676208#frequency_tab" }, { "id": "rs1238676208", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1238676208" } ], "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": "11", "chr_pos": "47284510", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S701", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8WXG6-1.689.689", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WXG6-1.692.692", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.699.699", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WXG6-1.707.707", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.709.709", "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": "Q8WXG6-1.707.707", "start_pos": 707, "end_pos": 707, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PDSENSQENPPLRSSSSTTA", "down_seq": "SSPSTVIHGANSEPADSTEM", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [ "n-glyco-sequon-gain", "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: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "11", "chr_pos": "47284528", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S707", "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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8WXG6-1.689.689", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WXG6-1.692.692", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.699.699", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WXG6-1.701.701", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.709.709", "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": "Q8WXG6-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VVFFCQPEGCLSVRQRRMSL", "down_seq": "DDTSFVFTLTDKDTGVTRYG", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "47274714", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R72", "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: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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.740.740", "start_pos": 740, "end_pos": 740, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "EPADSTEMDDKAAVGVSKPL", "down_seq": "SVPPSIGKSNVDRRQAEIGE", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "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": "11", "chr_pos": "47285001", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P740", "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: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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.791.791", "start_pos": 791, "end_pos": 791, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs188085430", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188085430", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs188085430", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188085430", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs188085430", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188085430", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs188085430", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188085430", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PYFEPQYGFPPEEDEDEQGE", "down_seq": "YTPRFSQHVSGNRAQKLLRP", "snv": [ { "evidence": [ { "id": "rs188085430", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188085430" }, { "id": "rs188085430", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188085430" }, { "id": "rs188085430", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188085430" }, { "id": "rs188085430", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188085430" } ], "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 (SYT->NYT).", "chr_id": "11", "chr_pos": "47285155", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S791", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q8WXG6-1.805.805", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WXG6-1.805.805", "start_pos": 805, "end_pos": 805, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751730956", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751730956", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751730956", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751730956", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751730956", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751730956#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751730956", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751730956", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs377417195", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377417195", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377417195", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377417195", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs377417195", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377417195#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs377417195", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377417195", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EDEQGESYTPRFSQHVSGNR", "down_seq": "QKLLRPNSLRLASDSDAESD", "snv": [ { "evidence": [ { "id": "rs751730956", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751730956" }, { "id": "rs751730956", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751730956" }, { "id": "rs751730956", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751730956#frequency_tab" }, { "id": "rs751730956", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751730956" }, { "id": "rs377417195", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377417195" }, { "id": "rs377417195", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377417195" }, { "id": "rs377417195", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377417195#frequency_tab" }, { "id": "rs377417195", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377417195" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRA->NRS).", "chr_id": "11", "chr_pos": "47285452", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A805", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8WXG6-1.791.791", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WXG6-1.818.818", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WXG6-1.820.820", "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": "Q8WXG6-1.818.818", "start_pos": 818, "end_pos": 818, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "rs1259138484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1259138484", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1259138484", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1259138484#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QHVSGNRAQKLLRPNSLRLA", "down_seq": "DSDAESDSRASSPNSTVSNT", "snv": [ { "evidence": [ { "id": "rs1259138484", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1259138484" }, { "id": "rs1259138484", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1259138484#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 (SDS->NDS).", "chr_id": "11", "chr_pos": "47285492", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S818", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "site_lbl": "Ser818" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8WXG6-1.805.805", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WXG6-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.826.826", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WXG6-1.834.834", "categories": [ "glycosylation_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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q8WXG6-1.908.908", "start_pos": 908, "end_pos": 908, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2063374491", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2063374491", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2063374491", "url": "https://www.ensembl.org/id/rs2063374491", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LNTLMEIVTEAGPGSGEGNR", "down_seq": "ALVDQKSSVIKHSPTVKREP", "snv": [ { "evidence": [ { "id": "rs2063374491", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2063374491" }, { "id": "rs2063374491", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2063374491" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRR->NRT).", "chr_id": "11", "chr_pos": "47289400", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R908", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8WXG6-1.914.914", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.916.916", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WXG6-1.921.921", "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": "Q8WXG6-1.914.914", "start_pos": 914, "end_pos": 914, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780773918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780773918", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780773918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780773918", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780773918", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780773918#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780773918", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780773918", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "IVTEAGPGSGEGNRRALVDQ", "down_seq": "SSVIKHSPTVKREPPSPQGR", "snv": [ { "evidence": [ { "id": "rs780773918", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780773918" }, { "id": "rs780773918", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780773918" }, { "id": "rs780773918", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780773918#frequency_tab" }, { "id": "rs780773918", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780773918" } ], "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": "11", "chr_pos": "47289996", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K914", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8WXG6-1.908.908", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.916.916", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WXG6-1.921.921", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WXG6-1.930.930", "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": "Q8WXG6-1.936.936", "start_pos": 936, "end_pos": 936, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs766181855", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766181855", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766181855", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766181855", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766181855", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766181855#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs766181855", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766181855", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SVIKHSPTVKREPPSPQGRS", "down_seq": "NSSENQQFLKEVVHSVLDGQ", "snv": [ { "evidence": [ { "id": "rs766181855", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766181855" }, { "id": "rs766181855", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766181855" }, { "id": "rs766181855", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766181855#frequency_tab" }, { "id": "rs766181855", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766181855" } ], "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 (SNS->NNS).", "chr_id": "11", "chr_pos": "47289484", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S936", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WXG6-1.916.916", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8WXG6-1.921.921", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WXG6-1.930.930", "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": "Q8WXG6-1.967.967", "start_pos": 967, "end_pos": 967, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EVVHSVLDGQGVGWLNMKKV", "down_seq": "RLLESEQLRVFVLSKLNRMV", "snv": [ { "evidence": [ { "id": "Q8WXG6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WXG6" } ], "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 (4).", "chr_id": "11", "chr_pos": "47289949", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R967", "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: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": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.1059.1059", "start_pos": 1059, "end_pos": 1059, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "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": "GLLEIAQTHYYSKEPDKRKR", "down_seq": "PTESVNTPVGKDPGLAGRGD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1059" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.1061.1061", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WXG6-1.1066.1066", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.1067.1067", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8WXG6-1.1061.1061", "start_pos": 1061, "end_pos": 1061, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LEIAQTHYYSKEPDKRKRSP", "down_seq": "ESVNTPVGKDPGLAGRGDPK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "site_lbl": "Thr1061" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.1059.1059", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WXG6-1.1066.1066", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WXG6-1.1067.1067", "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": "Q8WXG6-1.1066.1066", "start_pos": 1066, "end_pos": 1066, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "THYYSKEPDKRKRSPTESVN", "down_seq": "PVGKDPGLAGRGDPKAMAQL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "site_lbl": "Thr1066" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8WXG6-1.1059.1059", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WXG6-1.1061.1061", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8WXG6-1.1067.1067", "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": "Q8WXG6-1.1110.1110", "start_pos": 1110, "end_pos": 1110, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLGPRAPSATGKGPKELDTR", "down_seq": "LKEENFIASIELWNKHQEVK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "site_lbl": "Ser1110" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "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": "Q8WXG6-1.1174.1174", "start_pos": 1174, "end_pos": 1174, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "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": "EKKSQISADSGVSLTSSSQR", "down_seq": "DQDSVIGVSPAVMIRSSSQD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr1174" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8WXG6-1.1161.1161", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.1166.1166", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WXG6-1.1169.1169", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WXG6-1.1183.1183", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WXG6-1.1189.1189", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WXG6-1.1190.1190", "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": "Q8WXG6-1.1183.1183", "start_pos": 1183, "end_pos": 1183, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "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": "SGVSLTSSSQRTDQDSVIGV", "down_seq": "PAVMIRSSSQDSEVSTVVSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1183" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8WXG6-1.1166.1166", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WXG6-1.1169.1169", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WXG6-1.1174.1174", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WXG6-1.1189.1189", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WXG6-1.1190.1190", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8WXG6-1.1199.1199", "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": "Q8WXG6-1.1199.1199", "start_pos": 1199, "end_pos": 1199, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Mol. Cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Phosphoproteomic analysis of distinct tumor cell lines in response to nocodazole treatment.", "journal": "Proteomics", "date": "2009", "authors": "Nagano K, Shinkawa T, Mutoh H, Kondoh O, Morimoto S, Inomata N, Ashihara M, Ishii N, Aoki Y, Haramura M", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VIGVSPAVMIRSSSQDSEVS", "down_seq": "VVSNSSGETLGADSDLSSNA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ], "site_lbl": "Thr1199" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8WXG6-1.1183.1183", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WXG6-1.1189.1189", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WXG6-1.1190.1190", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8WXG6-1.1237.1237", "start_pos": 1237, "end_pos": 1237, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Mol. Cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Phosphoproteomic analysis of distinct tumor cell lines in response to nocodazole treatment.", "journal": "Proteomics", "date": "2009", "authors": "Nagano K, Shinkawa T, Mutoh H, Kondoh O, Morimoto S, Inomata N, Ashihara M, Ishii N, Aoki Y, Haramura M", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SNAGDGPGGEGSVHLASSRG", "down_seq": "LSDSEIETNSATSTIFGKAH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ], "site_lbl": "Thr1237" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8WXG6-1.1220.1220", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8WXG6-1.1226.1226", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WXG6-1.1239.1239", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8WXG6-1.1241.1241", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WXG6-1.1248.1248", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8WXG6-1.1241.1241", "start_pos": 1241, "end_pos": 1241, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "DGPGGEGSVHLASSRGTLSD", "down_seq": "EIETNSATSTIFGKAHSLKP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1241" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8WXG6-1.1226.1226", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WXG6-1.1237.1237", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.1239.1239", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WXG6-1.1248.1248", "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": "Q8WXG6-1.1270.1270", "start_pos": 1270, "end_pos": 1270, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STIFGKAHSLKPSIKEKLAG", "down_seq": "PIRTSEDVSQRVYLYEGLLG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser1270" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q8WXG6-1.1275.1275", "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": "Q8WXG6-1.1275.1275", "start_pos": 1275, "end_pos": 1275, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "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": "KAHSLKPSIKEKLAGSPIRT", "down_seq": "EDVSQRVYLYEGLLGRDKGS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1275" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8WXG6-1.1270.1270", "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": "Q8WXG6-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SESGSSLQPLSADSTPDVNQ", "down_seq": "PRGKRRAKAGSRSRNSTLTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "site_lbl": "Ser156" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WXG6-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8WXG6-1.138.138", "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": "Q8WXG6-1.689.689", "start_pos": 689, "end_pos": 689, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SEVEIDELQNQKEAEEPGPD", "down_seq": "ENSQENPPLRSSSSTTASSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "site_lbl": "Ser689" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8WXG6-1.692.692", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WXG6-1.699.699", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WXG6-1.701.701", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WXG6-1.707.707", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WXG6-1.709.709", "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": "Q8WXG6-1.692.692", "start_pos": 692, "end_pos": 692, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIDELQNQKEAEEPGPDSEN", "down_seq": "QENPPLRSSSSTTASSSPST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "site_lbl": "Ser692" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8WXG6-1.689.689", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WXG6-1.699.699", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WXG6-1.701.701", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WXG6-1.707.707", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8WXG6-1.709.709", "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": "Q8WXG6-1.709.709", "start_pos": 709, "end_pos": 709, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SENSQENPPLRSSSSTTASS", "down_seq": "PSTVIHGANSEPADSTEMDD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser709" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WXG6-1.689.689", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8WXG6-1.692.692", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8WXG6-1.699.699", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.701.701", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.707.707", "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": "Q8WXG6-1.813.813", "start_pos": 813, "end_pos": 813, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPRFSQHVSGNRAQKLLRPN", "down_seq": "LRLASDSDAESDSRASSPNS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "site_lbl": "Ser813" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.805.805", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WXG6-1.818.818", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WXG6-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WXG6-1.826.826", "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": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WXG6-1.820.820", "start_pos": 820, "end_pos": 820, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSGNRAQKLLRPNSLRLASD", "down_seq": "DAESDSRASSPNSTVSNTST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "site_lbl": "Ser820" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8WXG6-1.805.805", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WXG6-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.818.818", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WXG6-1.826.826", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WXG6-1.834.834", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8WXG6-1.848.848", "start_pos": 848, "end_pos": 848, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "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": "ASSPNSTVSNTSTEGFGGIM", "down_seq": "FASSLYRNHSTSFSLSNLTL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser848" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8WXG6-1.834.834", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8WXG6-1.856.856", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8WXG6-1.858.858", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WXG6-1.862.862", "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": "Q8WXG6-1.862.862", "start_pos": 862, "end_pos": 862, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GFGGIMSFASSLYRNHSTSF", "down_seq": "LSNLTLPTKGAREKATPFPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "site_lbl": "Ser862" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8WXG6-1.848.848", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8WXG6-1.856.856", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8WXG6-1.858.858", "categories": [ "snv_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": "Q8WXG6-1.916.916", "start_pos": 916, "end_pos": 916, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TEAGPGSGEGNRRALVDQKS", "down_seq": "VIKHSPTVKREPPSPQGRSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "site_lbl": "Ser916" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8WXG6-1.908.908", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8WXG6-1.914.914", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8WXG6-1.921.921", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WXG6-1.930.930", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WXG6-1.936.936", "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": "Q8WXG6-1.921.921", "start_pos": 921, "end_pos": 921, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "iPTMnet", "id": "Q8WXG6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSGEGNRRALVDQKSSVIKH", "down_seq": "PTVKREPPSPQGRSSNSSEN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q8WXG6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WXG6" } ], "site_lbl": "Ser921" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8WXG6-1.908.908", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WXG6-1.914.914", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8WXG6-1.916.916", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8WXG6-1.930.930", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WXG6-1.936.936", "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": "Q8WXG6-1.930.930", "start_pos": 930, "end_pos": 930, "uniprot_canonical_ac": "Q8WXG6-1", "length": 1647, "uniprot_id": "MADD_HUMAN", "protein_name": "MAP kinase-activating death domain protein", "refseq_ac": "NP_569826", "refseq_name": "MAP kinase-activating death domain protein isoform 1", "gene_name": "MADD", "gene_names_uniprotkb": "MADD; DENN; IG20; KIAA0358", "gene_names_refseq": "DEEAH; DENN; IG20; MADD; NEDDISH; RAB3GEP; RabGEF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LVDQKSSVIKHSPTVKREPP", "down_seq": "PQGRSSNSSENQQFLKEVVH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WXG6", "url": "https://www.uniprot.org/uniprotkb/Q8WXG6" } ], "site_lbl": "Ser930" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "856", "end_pos": "856" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "1067", "end_pos": "1067" }, { "start_pos": "1161", "end_pos": "1161" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1169", "end_pos": "1169" }, { "start_pos": "1189", "end_pos": "1189" }, { "start_pos": "1190", "end_pos": "1190" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1248", "end_pos": "1248" }, { "start_pos": "1369", "end_pos": "1369" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1485", "end_pos": "1485" }, { "start_pos": "1516", "end_pos": "1516" }, { "start_pos": "1532", "end_pos": "1532" }, { "start_pos": "1589", "end_pos": "1589" }, { "start_pos": "1621", "end_pos": "1621" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "701", "end_pos": "701" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "805", "end_pos": "805" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "856", "end_pos": "856" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "936", "end_pos": "936" }, { "start_pos": "967", "end_pos": "967" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1199", "end_pos": "1199" }, { "start_pos": "1237", "end_pos": "1237" }, { "start_pos": "1239", "end_pos": "1239" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "848", "end_pos": "848" }, { "start_pos": "858", "end_pos": "858" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "930", "end_pos": "930" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8WXG6-1.914.914", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8WXG6-1.916.916", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8WXG6-1.921.921", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8WXG6-1.936.936", "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": "Q6DN14-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "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": "rs922488628", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs922488628", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs922488628", "url": "https://www.ensembl.org/id/rs922488628", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "REHLLPAVKGPAAASGAAGG", "down_seq": "PPGGRSPDSAPSSSSASSSL", "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": "Thr146", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs922488628", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs922488628" }, { "id": "rs922488628", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs922488628" } ], "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": "5", "chr_pos": "95284140", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T146", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q6DN14-1.152.152", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6DN14-1.158.158", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6DN14-1.161.161", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6DN14-1.733.733", "start_pos": 733, "end_pos": 733, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "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": "SIQNGEQKAYVLKNKQLTGP", "down_seq": "KGVIYLEIDVIFNAVKASLR", "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": "Thr733", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs960951918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs960951918", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs960951918", "url": "https://www.ncbi.nlm.nih.gov/snp/rs960951918#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RARDEGARRQGPGAHLCHQK", "down_seq": "SSLPGTACLEQLLEPPPPPA", "snv": [ { "evidence": [ { "id": "rs960951918", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs960951918" }, { "id": "rs960951918", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs960951918#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 (SSS->NSS).", "chr_id": "5", "chr_pos": "95283983", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S198", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs868241044", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868241044", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs868241044", "url": "https://www.ensembl.org/id/rs868241044", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "NAEVPLADPGMYQLDITLRR", "down_seq": "QSLAARDRGGTSDPYVKFKI", "snv": [ { "evidence": [ { "id": "rs868241044", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868241044" }, { "id": "rs868241044", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs868241044" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (GQS->NQS).", "chr_id": "5", "chr_pos": "95017396_95017397delin", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G270", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.346.346", "start_pos": 346, "end_pos": 346, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs937844723", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs937844723", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs937844723", "url": "https://www.ncbi.nlm.nih.gov/snp/rs937844723#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs937844723", "url": "http://gnomad.broadinstitute.org/awesome?query=rs937844723", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs937844723", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs937844723", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "IKVFDYDFGLQDDFMGSAFL", "down_seq": "LTQLELNRPTDVTLTLKDPH", "snv": [ { "evidence": [ { "id": "rs937844723", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs937844723" }, { "id": "rs937844723", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs937844723#frequency_tab" }, { "id": "rs937844723", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs937844723" }, { "id": "rs937844723", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs937844723" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DLT->NLT).", "chr_id": "5", "chr_pos": "94942373", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D346", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q6DN14-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6DN14-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6DN14-1.359.359", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6DN14-1.355.355", "start_pos": 355, "end_pos": 355, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs914526220", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs914526220", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs914526220", "url": "https://www.ncbi.nlm.nih.gov/snp/rs914526220#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs914526220", "url": "http://gnomad.broadinstitute.org/awesome?query=rs914526220", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LQDDFMGSAFLDLTQLELNR", "down_seq": "TDVTLTLKDPHYPDHDLGII", "snv": [ { "evidence": [ { "id": "rs914526220", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs914526220" }, { "id": "rs914526220", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs914526220#frequency_tab" }, { "id": "rs914526220", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs914526220" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRP->NRS).", "chr_id": "5", "chr_pos": "94940194", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P355", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NRP->NRT).", "chr_id": "5", "chr_pos": "94940194", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P355", "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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q6DN14-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6DN14-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6DN14-1.359.359", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q6DN14-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs933102624", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs933102624", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs933102624", "url": "https://www.ncbi.nlm.nih.gov/snp/rs933102624#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs933102624", "url": "http://gnomad.broadinstitute.org/awesome?query=rs933102624", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs933102624", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs933102624", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DDFMGSAFLDLTQLELNRPT", "down_seq": "VTLTLKDPHYPDHDLGIILL", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" }, { "id": "rs933102624", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs933102624" }, { "id": "rs933102624", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs933102624#frequency_tab" }, { "id": "rs933102624", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs933102624" }, { "id": "rs933102624", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs933102624" } ], "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 (DVT->NVT).", "chr_id": "5", "chr_pos": "94940188", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D357", "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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6DN14-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6DN14-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6DN14-1.359.359", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6DN14-1.359.359", "start_pos": 359, "end_pos": 359, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1359592236", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1359592236", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1359592236", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1359592236", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FMGSAFLDLTQLELNRPTDV", "down_seq": "LTLKDPHYPDHDLGIILLSV", "snv": [ { "evidence": [ { "id": "rs1359592236", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1359592236" }, { "id": "rs1359592236", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1359592236" } ], "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": "5", "chr_pos": "94940181", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T359", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6DN14-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6DN14-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6DN14-1.357.357", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6DN14-1.390.390", "start_pos": 390, "end_pos": 390, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1817206325", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1817206325", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1817206325", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1817206325#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1817206325", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1817206325", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HDLGIILLSVILTPKEGESR", "down_seq": "VTMLMRKSWKRSSKELSENE", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" }, { "id": "rs1817206325", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1817206325" }, { "id": "rs1817206325", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1817206325#frequency_tab" }, { "id": "rs1817206325", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1817206325" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DVT->NVT).", "chr_id": "5", "chr_pos": "94940089", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D390", "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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.415.415", "start_pos": 415, "end_pos": 415, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MRKSWKRSSKELSENEVVGS", "down_seq": "FSVKSLFWRTCGRPALPVLG", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Y", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (YFS->NFS).", "chr_id": "5", "chr_pos": "94923991", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Y415", "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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q6DN14-1.427.427", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6DN14-1.427.427", "start_pos": 427, "end_pos": 427, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SENEVVGSYFSVKSLFWRTC", "down_seq": "RPALPVLGFCRAELQNPYCK", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "5", "chr_pos": "94917967", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G427", "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: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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q6DN14-1.415.415", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6DN14-1.473.473", "start_pos": 473, "end_pos": 473, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TQSLRLSDLHRKSHLWRGIV", "down_seq": "ITLIEGRDLKAMDSNGLSDP", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "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 (SIT->NIT).", "chr_id": "5", "chr_pos": "94912909", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S473", "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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.555.555", "start_pos": 555, "end_pos": 555, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs998582409", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs998582409", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs998582409", "url": "https://www.ncbi.nlm.nih.gov/snp/rs998582409#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs998582409", "url": "http://gnomad.broadinstitute.org/awesome?query=rs998582409", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs998582409", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs998582409", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ITAWDKDAGKRDDFIGRCQV", "down_seq": "LSALSREQTHKLELQLEEGE", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" }, { "id": "rs998582409", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs998582409" }, { "id": "rs998582409", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs998582409#frequency_tab" }, { "id": "rs998582409", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs998582409" }, { "id": "rs998582409", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs998582409" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "5", "chr_pos": "94894825", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D555", "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: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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.591.591", "start_pos": 591, "end_pos": 591, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LEEGEGHLVLLVTLTASATV", "down_seq": "ISDLSVNSLEDQKEREEILK", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "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 (SIS->NIS).", "chr_id": "5", "chr_pos": "94894716", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S591", "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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.642.642", "start_pos": 642, "end_pos": 642, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748879228", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748879228", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748879228", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748879228", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748879228", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748879228", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LKDVGFLQVKVIRAEGLMAA", "down_seq": "VTGKSDPFCVVELNNDRLLT", "snv": [ { "evidence": [ { "id": "rs748879228", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748879228" }, { "id": "rs748879228", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748879228" }, { "id": "rs748879228", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748879228" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DVT->NVT).", "chr_id": "5", "chr_pos": "94888888", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D642", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.670.670", "start_pos": 670, "end_pos": 670, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758675904", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758675904", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758675904", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758675904", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758675904", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758675904#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs758675904", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758675904", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FCVVELNNDRLLTHTVYKNL", "down_seq": "PEWNKVFTFNIKDIHSVLEV", "snv": [ { "evidence": [ { "id": "rs758675904", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758675904" }, { "id": "rs758675904", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758675904" }, { "id": "rs758675904", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758675904#frequency_tab" }, { "id": "rs758675904", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758675904" } ], "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": "5", "chr_pos": "94873166", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N670", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.697.697", "start_pos": 697, "end_pos": 697, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FTFNIKDIHSVLEVTVYDED", "down_seq": "DRSADFLGKVAIPLLSIQNG", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "94871365", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R697", "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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q6DN14-1.698.698", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6DN14-1.699.699", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6DN14-1.698.698", "start_pos": 698, "end_pos": 698, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TFNIKDIHSVLEVTVYDEDR", "down_seq": "RSADFLGKVAIPLLSIQNGE", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "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": "5", "chr_pos": "94871362", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D698", "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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q6DN14-1.697.697", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6DN14-1.699.699", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6DN14-1.699.699", "start_pos": 699, "end_pos": 699, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FNIKDIHSVLEVTVYDEDRD", "down_seq": "SADFLGKVAIPLLSIQNGEQ", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "5", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "94871359", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R699", "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: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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q6DN14-1.697.697", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6DN14-1.698.698", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6DN14-1.761.761", "start_pos": 761, "end_pos": 761, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "IDVIFNAVKASLRTLIPKEQ", "down_seq": "YIEEENRLSKQLLLRNFIRM", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "5", "chr_pos": "94870450", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K761", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q6DN14-1.773.773", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6DN14-1.773.773", "start_pos": 773, "end_pos": 773, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "RTLIPKEQKYIEEENRLSKQ", "down_seq": "LLRNFIRMKRCVMVLVNAAY", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "94868451", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L773", "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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q6DN14-1.761.761", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6DN14-1.861.861", "start_pos": 861, "end_pos": 861, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "IISGKDNRQRDTVVEDMLED", "down_seq": "EEEDDKDDKDSEKKGFINKI", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "5", "chr_pos": "94779139", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E861", "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: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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.903.903", "start_pos": 903, "end_pos": 903, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AIQEVCVSVQNILDEVASFG", "down_seq": "RIKNTFNWTVPFLSWLAIVA", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "94714790", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E903", "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: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": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q6DN14-1.906.906", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6DN14-1.909.909", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6DN14-1.906.906", "start_pos": 906, "end_pos": 906, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6DN14", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1758469696", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1758469696", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1758469696", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1758469696#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1758469696", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1758469696", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1758469696", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1758469696", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EVCVSVQNILDEVASFGERI", "down_seq": "NTFNWTVPFLSWLAIVALCV", "snv": [ { "evidence": [ { "id": "Q6DN14", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6DN14" }, { "id": "rs1758469696", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1758469696" }, { "id": "rs1758469696", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1758469696#frequency_tab" }, { "id": "rs1758469696", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1758469696" }, { "id": "rs1758469696", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1758469696" } ], "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 (KNT->NNT).", "chr_id": "5", "chr_pos": "94714779", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K906", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q6DN14-1.903.903", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6DN14-1.909.909", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q6DN14-1.909.909", "start_pos": 909, "end_pos": 909, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs754984567", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754984567", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754984567", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754984567", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754984567", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754984567", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "VSVQNILDEVASFGERIKNT", "down_seq": "NWTVPFLSWLAIVALCVFTA", "snv": [ { "evidence": [ { "id": "rs754984567", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754984567" }, { "id": "rs754984567", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754984567" }, { "id": "rs754984567", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754984567" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTF->NTS).", "chr_id": "5", "chr_pos": "94710922", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F909", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q6DN14-1.903.903", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6DN14-1.906.906", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6DN14-1.999.999", "start_pos": 999, "end_pos": 999, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1754947495", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1754947495", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1754947495", "url": "https://www.ensembl.org/id/rs1754947495", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YQELKPDPSHSPYKRKKNNL", "down_seq": "", "snv": [ { "evidence": [ { "id": "rs1754947495", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1754947495" }, { "id": "rs1754947495", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1754947495" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLG->NLC).", "chr_id": "5", "chr_pos": "94707501", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G999", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "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": "Q6DN14-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteomic analysis of human brain by calcium phosphate precipitation and mass spectrometry.", "journal": "Journal of proteome research", "date": "2008", "authors": "Xia Q, Cheng D, Duong DM, Gearing M, Lah JJ, Levey AI, Peng J", "evidence": [ { "database": "iPTMnet", "id": "Q6DN14-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6DN14-1" } ], "reference": [ { "type": "PubMed", "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355" } ] } ], "crossref": [ { "id": "Q6DN14", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6DN14", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AVKGPAAASGAAGGTPPGGR", "down_seq": "PDSAPSSSSASSSLSSSPQP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6DN14", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6DN14" }, { "database": "PubMed", "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355" } ], "site_lbl": "Ser152" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q6DN14-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6DN14-1.158.158", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6DN14-1.161.161", "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": "Q6DN14-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteomic analysis of human brain by calcium phosphate precipitation and mass spectrometry.", "journal": "Journal of proteome research", "date": "2008", "authors": "Xia Q, Cheng D, Duong DM, Gearing M, Lah JJ, Levey AI, Peng J", "evidence": [ { "database": "iPTMnet", "id": "Q6DN14-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6DN14-1" } ], "reference": [ { "type": "PubMed", "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355" } ] } ], "crossref": [ { "id": "Q6DN14", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6DN14", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AASGAAGGTPPGGRSPDSAP", "down_seq": "SSSASSSLSSSPQPPPRGDR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6DN14", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6DN14" }, { "database": "PubMed", "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355" } ], "site_lbl": "Ser158" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q6DN14-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6DN14-1.152.152", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6DN14-1.161.161", "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": "Q6DN14-1.161.161", "start_pos": 161, "end_pos": 161, "uniprot_canonical_ac": "Q6DN14-1", "length": 999, "uniprot_id": "MCTP1_HUMAN", "protein_name": "Multiple C2 and transmembrane domain-containing protein 1", "refseq_ac": "NP_001002796", "refseq_name": "multiple C2 and transmembrane domain-containing protein 1 isoform S", "gene_name": "MCTP1", "gene_names_uniprotkb": "MCTP1", "gene_names_refseq": "MCTP1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6DN14", "url": "https://www.uniprot.org/uniprotkb/Q6DN14" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteomic analysis of human brain by calcium phosphate precipitation and mass spectrometry.", "journal": "Journal of proteome research", "date": "2008", "authors": "Xia Q, Cheng D, Duong DM, Gearing M, Lah JJ, Levey AI, Peng J", "evidence": [ { "database": "iPTMnet", "id": "Q6DN14-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6DN14-1" } ], "reference": [ { "type": "PubMed", "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355" } ] } ], "crossref": [ { "id": "Q6DN14", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6DN14", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAAGGTPPGGRSPDSAPSSS", "down_seq": "ASSSLSSSPQPPPRGDRARD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6DN14", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6DN14" }, { "database": "PubMed", "id": "18510355", "url": "https://glygen.org/publication/PubMed/18510355" } ], "site_lbl": "Ser161" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "733", "end_pos": "733" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "698", "end_pos": "698" }, { "start_pos": "699", "end_pos": "699" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "906", "end_pos": "906" }, { "start_pos": "909", "end_pos": "909" }, { "start_pos": "999", "end_pos": "999" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6DN14-1.146.146", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q6DN14-1.152.152", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6DN14-1.158.158", "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": "Q99638-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "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": "rs547310292", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547310292", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs547310292", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs547310292", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs547310292", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547310292", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs547310292", "url": "http://gnomad.broadinstitute.org/awesome?query=rs547310292", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RSAYACFLFAPLFFQQYQAA", "down_seq": "PGQDLLRCKILMKSFLSVFR", "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": "Thr65", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs547310292", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547310292" }, { "id": "rs547310292", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs547310292" }, { "id": "rs547310292", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547310292" }, { "id": "rs547310292", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs547310292" } ], "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": "11", "chr_pos": "67392742", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T65", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q99638-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Multi-comparative Thermal Proteome Profiling Uncovers New O-GlcNAc Proteins in a System-wide Method.", "journal": "Analytical chemistry", "date": "2022-12-29", "authors": "Wang Guoli, Li Yang, Wang Ting, Wang Jun, Yao Jun, Yan Guoquan, Zhang Ying, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q99638", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q99638" } ], "reference": [ { "type": "PubMed", "id": "36580660", "url": "https://glygen.org/publication/PubMed/36580660" } ] }, { "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": "Q99638", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q99638" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "crossref": [ { "id": "36580660", "url": "https://glygen.org/publication/PubMed/36580660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q99638", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q99638", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "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": "36580660", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36580660" }, { "id": "Q99638", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q99638" }, { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "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" ] } ] }, { "id": "Q99638-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of human Rad9 is required for genotoxin-activated checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Roos-Mattjus P, Hopkins KM, Oestreich AJ, Vroman BT, Johnson KL, Naylor S, Lieberman HB, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] }, { "title": "ATM-dependent phosphorylation of human Rad9 is required for ionizing radiation-induced checkpoint activation.", "journal": "The Journal of biological chemistry", "date": "2001", "authors": "Chen MJ, Lin YT, Lieberman HB, Chen G, Lee EY", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "11278446", "url": "https://glygen.org/publication/PubMed/11278446" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "DNA damage-dependent and -independent phosphorylation of the hRad9 checkpoint protein.", "journal": "The Journal of biological chemistry", "date": "2001", "authors": "St Onge RP, Besley BD, Park M, Casselman R, Davey S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "11551919", "url": "https://glygen.org/publication/PubMed/11551919" } ] }, { "title": "Rad9 modulates the P21WAF1 pathway by direct association with p53.", "journal": "BMC molecular biology", "date": "2007", "authors": "Ishikawa K, Ishii H, Murakumo Y, Mimori K, Kobayashi M, Yamamoto K, Mori M, Nishino H, Furukawa Y, Ichimura K", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "17511890", "url": "https://glygen.org/publication/PubMed/17511890" } ] }, { "title": "Chk1 Activation Protects Rad9A from Degradation as Part of a Positive Feedback Loop during Checkpoint Signalling.", "journal": "PloS one", "date": "2015", "authors": "Osorio-Zambrano WF, Davey S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "26658951", "url": "https://glygen.org/publication/PubMed/26658951" } ] } ], "crossref": [ { "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11278446", "url": "https://glygen.org/publication/PubMed/11278446", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11551919", "url": "https://glygen.org/publication/PubMed/11551919", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17511890", "url": "https://glygen.org/publication/PubMed/17511890", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26658951", "url": "https://glygen.org/publication/PubMed/26658951", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KDSLLDGHFVLATLSDTDSH", "down_seq": "QDLGSPERHQPVPQLQAHST", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Complete loss of phosphorylation and no loss of interaction with the 9-1-1 complex; when associated with A-277; A-328; A-341; A-375; A-380 and A-387.", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q13315-1", "kinase_gene_name": "ATM", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "11278446", "url": "https://glygen.org/publication/PubMed/11278446" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser272" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "11278446", "url": "https://glygen.org/publication/PubMed/11278446" }, { "database": "PubMed", "id": "11551919", "url": "https://glygen.org/publication/PubMed/11551919" }, { "database": "PubMed", "id": "17511890", "url": "https://glygen.org/publication/PubMed/17511890" }, { "database": "PubMed", "id": "26658951", "url": "https://glygen.org/publication/PubMed/26658951" } ], "site_lbl": "Ser272" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q99638-1.266.266", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q99638-1.270.270", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q99638-1.277.277", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q99638-1.292.292", "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": 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": "Q99638-1.277.277", "start_pos": 277, "end_pos": 277, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of human Rad9 is required for genotoxin-activated checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Roos-Mattjus P, Hopkins KM, Oestreich AJ, Vroman BT, Johnson KL, Naylor S, Lieberman HB, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] }, { "title": "A role for the phosphorylation of hRad9 in checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "St Onge RP, Besley BD, Pelley JL, Davey S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "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": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "DNA damage repair genes controlling human papillomavirus (HPV) episome levels under conditions of stability and extreme instability.", "journal": "PloS one", "date": "2013", "authors": "Edwards TG, Vidmar TJ, Koeller K, Bashkin JK, Fisher C", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "24098381", "url": "https://glygen.org/publication/PubMed/24098381" } ] }, { "title": "The CDK-PLK1 axis targets the DNA damage checkpoint sensor protein RAD9 to promote cell proliferation and tolerance to genotoxic stress.", "journal": "eLife", "date": "2017", "authors": "Wakida T, Ikura M, Kuriya K, Ito S, Shiroiwa Y, Habu T, Kawamoto T, Okumura K, Ikura T, Furuya K", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ] } ], "crossref": [ { "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24098381", "url": "https://glygen.org/publication/PubMed/24098381", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DGHFVLATLSDTDSHSQDLG", "down_seq": "PERHQPVPQLQAHSTPHPDD", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Complete loss of phosphorylation and no loss of interaction with the 9-1-1 complex; when associated with A-272; A-328; A-341; A-375; A-380 and A-387.", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06493-1", "kinase_gene_name": "CDK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ], "site_lbl": "Ser277" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "24098381", "url": "https://glygen.org/publication/PubMed/24098381" }, { "database": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ], "site_lbl": "Ser277" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q99638-1.266.266", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q99638-1.270.270", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q99638-1.272.272", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q99638-1.292.292", "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": 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": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q99638-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "c-Abl tyrosine kinase regulates the human Rad9 checkpoint protein in response to DNA damage.", "journal": "Molecular and cellular biology", "date": "2002", "authors": "Yoshida K, Komatsu K, Wang HG, Kufe D", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "11971963", "url": "https://glygen.org/publication/PubMed/11971963" } ] }, { "title": "Phosphorylation sites on Tyr28 and the C-terminus of Rad9 are required for inhibition of premature chromosomal condensation across the entire S phase.", "journal": "Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology", "date": "2008", "authors": "Zhang C, Zhang CX, He Y, Hang H", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "18769057", "url": "https://glygen.org/publication/PubMed/18769057" } ] } ], "crossref": [ { "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11971963", "url": "https://glygen.org/publication/PubMed/11971963", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18769057", "url": "https://glygen.org/publication/PubMed/18769057", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "GNVKVLGKAVHSLSRIGDEL", "down_seq": "LEPLEDGLSLRTVNSSRSAY", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Abolishes phosphorylation by ABL1.", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "11971963", "url": "https://glygen.org/publication/PubMed/11971963" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00519-1", "kinase_gene_name": "ABL1", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "11971963", "url": "https://glygen.org/publication/PubMed/11971963" } ], "site_lbl": "Tyr28" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "11971963", "url": "https://glygen.org/publication/PubMed/11971963" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "18769057", "url": "https://glygen.org/publication/PubMed/18769057" } ], "site_lbl": "Tyr28" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q99638-1.328.328", "start_pos": 328, "end_pos": 328, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of human Rad9 is required for genotoxin-activated checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Roos-Mattjus P, Hopkins KM, Oestreich AJ, Vroman BT, Johnson KL, Naylor S, Lieberman HB, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] }, { "title": "A role for the phosphorylation of hRad9 in checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "St Onge RP, Besley BD, Pelley JL, Davey S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ] }, { "title": "Phosphorylation of Rad9 at serine 328 by cyclin A-Cdk2 triggers apoptosis via interfering Bcl-xL.", "journal": "PloS one", "date": "2012", "authors": "Zhan Z, He K, Zhu D, Jiang D, Huang YH, Li Y, Sun C, Jin YH", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "23028682", "url": "https://glygen.org/publication/PubMed/23028682" } ] }, { "title": "Tousled homolog, TLK1, binds and phosphorylates Rad9; TLK1 acts as a molecular chaperone in DNA repair.", "journal": "DNA repair", "date": "2009", "authors": "Sunavala-Dossabhoy G, De Benedetti A", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "18940270", "url": "https://glygen.org/publication/PubMed/18940270" } ] }, { "title": "Tousled-like kinase-dependent phosphorylation of Rad9 plays a role in cell cycle progression and G2/M checkpoint exit.", "journal": "PloS one", "date": "2013", "authors": "Kelly R, Davey SK", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "24376897", "url": "https://glygen.org/publication/PubMed/24376897" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phenothiazine Inhibitors of TLKs Affect Double-Strand Break Repair and DNA Damage Response Recovery and Potentiate Tumor Killing with Radiomimetic Therapy.", "journal": "Genes & cancer", "date": "2013", "authors": "Ronald S, Awate S, Rath A, Carroll J, Galiano F, Dwyer D, Kleiner-Hancock H, Mathis JM, Vigod S, De Benedetti A", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "23946870", "url": "https://glygen.org/publication/PubMed/23946870" } ] }, { "title": "TLK1B mediated phosphorylation of Rad9 regulates its nuclear/cytoplasmic localization and cell cycle checkpoint.", "journal": "BMC molecular biology", "date": "2016", "authors": "Awate S, De Benedetti A", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "26860083", "url": "https://glygen.org/publication/PubMed/26860083" } ] }, { "title": "The CDK-PLK1 axis targets the DNA damage checkpoint sensor protein RAD9 to promote cell proliferation and tolerance to genotoxic stress.", "journal": "eLife", "date": "2017", "authors": "Wakida T, Ikura M, Kuriya K, Ito S, Shiroiwa Y, Habu T, Kawamoto T, Okumura K, Ikura T, Furuya K", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ] } ], "crossref": [ { "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23028682", "url": "https://glygen.org/publication/PubMed/23028682", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18940270", "url": "https://glygen.org/publication/PubMed/18940270", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24376897", "url": "https://glygen.org/publication/PubMed/24376897", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23946870", "url": "https://glygen.org/publication/PubMed/23946870", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26860083", "url": "https://glygen.org/publication/PubMed/26860083", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IAMETTIGNEGSRVLPSISL", "down_seq": "PGPQPPKSPGPHSEEEDEAE", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Complete loss of phosphorylation and no loss of interaction with the 9-1-1 complex; when associated with A-272; A-277; A-341; A-375; A-380 and A-387.", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06493-1", "kinase_gene_name": "CDK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ], "site_lbl": "Ser328" }, { "kinase_uniprot_canonical_ac": "P24941-1", "kinase_gene_name": "CDK2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "23028682", "url": "https://glygen.org/publication/PubMed/23028682" } ], "site_lbl": "Ser328" }, { "kinase_uniprot_canonical_ac": "Q9UKI8-1", "kinase_gene_name": "TLK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "18940270", "url": "https://glygen.org/publication/PubMed/18940270" }, { "database": "PubMed", "id": "24376897", "url": "https://glygen.org/publication/PubMed/24376897" } ], "site_lbl": "Ser328" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "18940270", "url": "https://glygen.org/publication/PubMed/18940270" }, { "database": "PubMed", "id": "23028682", "url": "https://glygen.org/publication/PubMed/23028682" }, { "database": "PubMed", "id": "23946870", "url": "https://glygen.org/publication/PubMed/23946870" }, { "database": "PubMed", "id": "24376897", "url": "https://glygen.org/publication/PubMed/24376897" }, { "database": "PubMed", "id": "26860083", "url": "https://glygen.org/publication/PubMed/26860083" }, { "database": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ], "site_lbl": "Ser328" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q99638-1.313.313", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q99638-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q99638-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q99638-1.326.326", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q99638-1.336.336", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q99638-1.341.341", "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": 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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q99638-1.341.341", "start_pos": 341, "end_pos": 341, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of human Rad9 is required for genotoxin-activated checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Roos-Mattjus P, Hopkins KM, Oestreich AJ, Vroman BT, Johnson KL, Naylor S, Lieberman HB, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] }, { "title": "Casein kinase 2-dependent phosphorylation of human Rad9 mediates the interaction between human Rad9-Hus1-Rad1 complex and TopBP1.", "journal": "Genes to cells : devoted to molecular & cellular mechanisms", "date": "2010", "authors": "Takeishi Y, Ohashi E, Ogawa K, Masai H, Obuse C, Tsurimoto T", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "20545769", "url": "https://glygen.org/publication/PubMed/20545769" } ] }, { "title": "Two serine phosphorylation sites in the C-terminus of Rad9 are critical for 9-1-1 binding to TopBP1 and activation of the DNA damage checkpoint response in HeLa cells.", "journal": "Genes to cells : devoted to molecular & cellular mechanisms", "date": "2012", "authors": "Ueda S, Takeishi Y, Ohashi E, Tsurimoto T", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "22925454", "url": "https://glygen.org/publication/PubMed/22925454" } ] }, { "title": "Interaction between Rad9-Hus1-Rad1 and TopBP1 activates ATR-ATRIP and promotes TopBP1 recruitment to sites of UV-damage.", "journal": "DNA repair", "date": "2014", "authors": "Ohashi E, Takeishi Y, Ueda S, Tsurimoto T", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "25091155", "url": "https://glygen.org/publication/PubMed/25091155" } ] } ], "crossref": [ { "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20545769", "url": "https://glygen.org/publication/PubMed/20545769", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22925454", "url": "https://glygen.org/publication/PubMed/22925454", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25091155", "url": "https://glygen.org/publication/PubMed/25091155", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VLPSISLSPGPQPPKSPGPH", "down_seq": "EEEDEAEPSTVPGTPPPKKF", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Complete loss of phosphorylation and no loss of interaction with the 9-1-1 complex; when associated with A-272; A-277; A-328; A-375; A-380 and A-387. Abolished phosphorylation by CK2, preventing interaction with TOPBP1; when associated with A-387.", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "20545769", "url": "https://glygen.org/publication/PubMed/20545769" } ] }, { "sequence_org": "S", "sequence_mut": "E", "comment": "Mimics phosphorylation, leading to weak but significant interaction with TOPBP1; when associated with E-387.", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "20545769", "url": "https://glygen.org/publication/PubMed/20545769" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by CK2", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "20545769", "url": "https://glygen.org/publication/PubMed/20545769" }, { "database": "PubMed", "id": "22925454", "url": "https://glygen.org/publication/PubMed/22925454" }, { "database": "PubMed", "id": "25091155", "url": "https://glygen.org/publication/PubMed/25091155" } ], "site_lbl": "Ser341" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q99638-1.326.326", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q99638-1.328.328", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q99638-1.336.336", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q99638-1.355.355", "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": "Q99638-1.375.375", "start_pos": 375, "end_pos": 375, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of human Rad9 is required for genotoxin-activated checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Roos-Mattjus P, Hopkins KM, Oestreich AJ, Vroman BT, Johnson KL, Naylor S, Lieberman HB, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPPPKKFRSLFFGSILAPVR", "down_seq": "PQGPSPVLAEDSEGEG", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Complete loss of phosphorylation and no loss of interaction with the 9-1-1 complex; when associated with A-272; A-277; A-328; A-341; A-380 and A-387.", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser375" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q99638-1.355.355", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q99638-1.380.380", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q99638-1.387.387", "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": 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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q99638-1.380.380", "start_pos": 380, "end_pos": 380, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of human Rad9 is required for genotoxin-activated checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Roos-Mattjus P, Hopkins KM, Oestreich AJ, Vroman BT, Johnson KL, Naylor S, Lieberman HB, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] }, { "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": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "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": "KFRSLFFGSILAPVRSPQGP", "down_seq": "PVLAEDSEGEG", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Complete loss of phosphorylation and no loss of interaction with the 9-1-1 complex; when associated with A-272; A-277; A-328; A-341; A-375 and A-387.", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser380" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q99638-1.375.375", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q99638-1.387.387", "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": 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": "Q99638-1.387.387", "start_pos": 387, "end_pos": 387, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of human Rad9 is required for genotoxin-activated checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Roos-Mattjus P, Hopkins KM, Oestreich AJ, Vroman BT, Johnson KL, Naylor S, Lieberman HB, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] }, { "title": "Casein kinase 2-dependent phosphorylation of human Rad9 mediates the interaction between human Rad9-Hus1-Rad1 complex and TopBP1.", "journal": "Genes to cells : devoted to molecular & cellular mechanisms", "date": "2010", "authors": "Takeishi Y, Ohashi E, Ogawa K, Masai H, Obuse C, Tsurimoto T", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "20545769", "url": "https://glygen.org/publication/PubMed/20545769" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "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": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "A role for the phosphorylation of hRad9 in checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "St Onge RP, Besley BD, Pelley JL, Davey S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ] }, { "title": "Structure and function of the Rad9-binding region of the DNA-damage checkpoint adaptor TopBP1.", "journal": "Nucleic acids research", "date": "2011", "authors": "Rappas M, Oliver AW, Pearl LH", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "20724438", "url": "https://glygen.org/publication/PubMed/20724438" } ] }, { "title": "Crystal structure of the N-terminal region of human Topoisomerase IIbeta binding protein 1.", "journal": "Biochemical and biophysical research communications", "date": "2010", "authors": "Huo YG, Bai L, Xu M, Jiang T", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "20858457", "url": "https://glygen.org/publication/PubMed/20858457" } ] }, { "title": "Two serine phosphorylation sites in the C-terminus of Rad9 are critical for 9-1-1 binding to TopBP1 and activation of the DNA damage checkpoint response in HeLa cells.", "journal": "Genes to cells : devoted to molecular & cellular mechanisms", "date": "2012", "authors": "Ueda S, Takeishi Y, Ohashi E, Tsurimoto T", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "22925454", "url": "https://glygen.org/publication/PubMed/22925454" } ] }, { "title": "Interaction between Rad9-Hus1-Rad1 and TopBP1 activates ATR-ATRIP and promotes TopBP1 recruitment to sites of UV-damage.", "journal": "DNA repair", "date": "2014", "authors": "Ohashi E, Takeishi Y, Ueda S, Tsurimoto T", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "25091155", "url": "https://glygen.org/publication/PubMed/25091155" } ] }, { "title": "Chk1 Activation Protects Rad9A from Degradation as Part of a Positive Feedback Loop during Checkpoint Signalling.", "journal": "PloS one", "date": "2015", "authors": "Osorio-Zambrano WF, Davey S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "26658951", "url": "https://glygen.org/publication/PubMed/26658951" } ] }, { "title": "BRCT domains of the DNA damage checkpoint proteins TOPBP1/Rad4 display distinct specificities for phosphopeptide ligands.", "journal": "eLife", "date": "2018", "authors": "Day M, Rappas M, Ptasinska K, Boos D, Oliver AW, Pearl LH", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "30295604", "url": "https://glygen.org/publication/PubMed/30295604" } ] }, { "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": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "The Rad9-Hus1-Rad1 (9-1-1) clamp activates checkpoint signaling via TopBP1.", "journal": "Genes & development", "date": "2007", "authors": "Delacroix S, Wagner JM, Kobayashi M, Yamamoto K, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "Reactome", "id": "R-HSA-5693607", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5693607" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "17575048", "url": "https://glygen.org/publication/PubMed/17575048" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20545769", "url": "https://glygen.org/publication/PubMed/20545769", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "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" ] }, { "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20724438", "url": "https://glygen.org/publication/PubMed/20724438", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20858457", "url": "https://glygen.org/publication/PubMed/20858457", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22925454", "url": "https://glygen.org/publication/PubMed/22925454", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25091155", "url": "https://glygen.org/publication/PubMed/25091155", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26658951", "url": "https://glygen.org/publication/PubMed/26658951", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30295604", "url": "https://glygen.org/publication/PubMed/30295604", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17575048", "url": "https://glygen.org/publication/PubMed/17575048", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSILAPVRSPQGPSPVLAED", "down_seq": "EGEG", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Complete loss of phosphorylation and no loss of interaction with the 9-1-1 complex; when associated with A-272; A-277; A-328; A-341; A-375 and A-380. Abolished phosphorylation by CK2, preventing interaction with TOPBP1; when associated with A-341.", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "20545769", "url": "https://glygen.org/publication/PubMed/20545769" } ] }, { "sequence_org": "S", "sequence_mut": "E", "comment": "Mimics phosphorylation, leading to weak but significant interaction with TOPBP1; when associated with E-341.", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "PubMed", "id": "20545769", "url": "https://glygen.org/publication/PubMed/20545769" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by CK2", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" }, { "database": "PubMed", "id": "20545769", "url": "https://glygen.org/publication/PubMed/20545769" }, { "database": "PubMed", "id": "20724438", "url": "https://glygen.org/publication/PubMed/20724438" }, { "database": "PubMed", "id": "20858457", "url": "https://glygen.org/publication/PubMed/20858457" }, { "database": "PubMed", "id": "22925454", "url": "https://glygen.org/publication/PubMed/22925454" }, { "database": "PubMed", "id": "25091155", "url": "https://glygen.org/publication/PubMed/25091155" }, { "database": "PubMed", "id": "26658951", "url": "https://glygen.org/publication/PubMed/26658951" }, { "database": "PubMed", "id": "30295604", "url": "https://glygen.org/publication/PubMed/30295604" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "17575048", "url": "https://glygen.org/publication/PubMed/17575048" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ], "site_lbl": "Ser387" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q99638-1.375.375", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q99638-1.380.380", "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": 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": 18 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q99638-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q99638", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99638", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FQDCESLQAVFDPASCPHML", "down_seq": "APARVLGEAVLPFSPALAEV", "snv": [ { "evidence": [ { "id": "Q99638", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99638" } ], "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 (4).", "chr_id": "11", "chr_pos": "67393778", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R146", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "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": "Q99638-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2134955546", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2134955546", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2134955546", "url": "https://www.ensembl.org/id/rs2134955546", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TLGIGRGRRVILRSYHEEEA", "down_seq": "STAKAMVTEMCLGEEDFQQL", "snv": [ { "evidence": [ { "id": "rs2134955546", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2134955546" }, { "id": "rs2134955546", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2134955546" } ], "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": "11", "chr_pos": "67395825", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D187", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "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": "Q99638-1.318.318", "start_pos": 318, "end_pos": 318, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746104003", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746104003", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746104003", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746104003", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746104003", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746104003#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs746104003", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746104003", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "FANDDIDSYMIAMETTIGNE", "down_seq": "SRVLPSISLSPGPQPPKSPG", "snv": [ { "evidence": [ { "id": "rs746104003", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746104003" }, { "id": "rs746104003", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746104003" }, { "id": "rs746104003", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746104003#frequency_tab" }, { "id": "rs746104003", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746104003" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEG->NEC).", "chr_id": "11", "chr_pos": "67397258", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G318", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746104003", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746104003" }, { "id": "rs746104003", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746104003" }, { "id": "rs746104003", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746104003#frequency_tab" }, { "id": "rs746104003", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746104003" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEG->NES).", "chr_id": "11", "chr_pos": "67397258", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G318", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q99638-1.313.313", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q99638-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q99638-1.326.326", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q99638-1.328.328", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q99638-1.336.336", "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": "Q99638-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q99638", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99638", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ANDDIDSYMIAMETTIGNEG", "down_seq": "RVLPSISLSPGPQPPKSPGP", "snv": [ { "evidence": [ { "id": "Q99638", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q99638" } ], "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": "11", "chr_pos": "67397262", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S319", "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: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": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q99638-1.313.313", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q99638-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q99638-1.326.326", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q99638-1.328.328", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q99638-1.336.336", "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": "Q99638-1.266.266", "start_pos": 266, "end_pos": 266, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "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": "PAIFTIKDSLLDGHFVLATL", "down_seq": "DTDSHSQDLGSPERHQPVPQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser266" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q99638-1.270.270", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q99638-1.272.272", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q99638-1.277.277", "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": "Q99638-1.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "TIKDSLLDGHFVLATLSDTD", "down_seq": "HSQDLGSPERHQPVPQLQAH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser270" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q99638-1.266.266", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q99638-1.272.272", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q99638-1.277.277", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q99638-1.292.292", "start_pos": 292, "end_pos": 292, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A role for the phosphorylation of hRad9 in checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "St Onge RP, Besley BD, Pelley JL, Davey S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ] }, { "title": "DNA damage-dependent and -independent phosphorylation of the hRad9 checkpoint protein.", "journal": "The Journal of biological chemistry", "date": "2001", "authors": "St Onge RP, Besley BD, Park M, Casselman R, Davey S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "11551919", "url": "https://glygen.org/publication/PubMed/11551919" } ] }, { "title": "The CDK-PLK1 axis targets the DNA damage checkpoint sensor protein RAD9 to promote cell proliferation and tolerance to genotoxic stress.", "journal": "eLife", "date": "2017", "authors": "Wakida T, Ikura M, Kuriya K, Ito S, Shiroiwa Y, Habu T, Kawamoto T, Okumura K, Ikura T, Furuya K", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ] } ], "crossref": [ { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11551919", "url": "https://glygen.org/publication/PubMed/11551919", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SQDLGSPERHQPVPQLQAHS", "down_seq": "PHPDDFANDDIDSYMIAMET", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06493-1", "kinase_gene_name": "CDK1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ], "site_lbl": "Thr292" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "11551919", "url": "https://glygen.org/publication/PubMed/11551919" }, { "database": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ], "site_lbl": "Thr292" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q99638-1.272.272", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q99638-1.277.277", "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": 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": "Q99638-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The CDK-PLK1 axis targets the DNA damage checkpoint sensor protein RAD9 to promote cell proliferation and tolerance to genotoxic stress.", "journal": "eLife", "date": "2017", "authors": "Wakida T, Ikura M, Kuriya K, Ito S, Shiroiwa Y, Habu T, Kawamoto T, Okumura K, Ikura T, Furuya K", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ] } ], "crossref": [ { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PHPDDFANDDIDSYMIAMET", "down_seq": "IGNEGSRVLPSISLSPGPQP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ], "site_lbl": "Thr313" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q99638-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q99638-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q99638-1.326.326", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q99638-1.328.328", "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": "Q99638-1.326.326", "start_pos": 326, "end_pos": 326, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The CDK-PLK1 axis targets the DNA damage checkpoint sensor protein RAD9 to promote cell proliferation and tolerance to genotoxic stress.", "journal": "eLife", "date": "2017", "authors": "Wakida T, Ikura M, Kuriya K, Ito S, Shiroiwa Y, Habu T, Kawamoto T, Okumura K, Ikura T, Furuya K", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ] } ], "crossref": [ { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YMIAMETTIGNEGSRVLPSI", "down_seq": "LSPGPQPPKSPGPHSEEEDE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ], "site_lbl": "Ser326" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q99638-1.313.313", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q99638-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q99638-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q99638-1.328.328", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q99638-1.336.336", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q99638-1.341.341", "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": "Q99638-1.336.336", "start_pos": 336, "end_pos": 336, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A role for the phosphorylation of hRad9 in checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "St Onge RP, Besley BD, Pelley JL, Davey S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ] }, { "title": "Phosphorylation of human Rad9 is required for genotoxin-activated checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Roos-Mattjus P, Hopkins KM, Oestreich AJ, Vroman BT, Johnson KL, Naylor S, Lieberman HB, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] }, { "title": "The CDK-PLK1 axis targets the DNA damage checkpoint sensor protein RAD9 to promote cell proliferation and tolerance to genotoxic stress.", "journal": "eLife", "date": "2017", "authors": "Wakida T, Ikura M, Kuriya K, Ito S, Shiroiwa Y, Habu T, Kawamoto T, Okumura K, Ikura T, Furuya K", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ] } ], "crossref": [ { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NEGSRVLPSISLSPGPQPPK", "down_seq": "PGPHSEEEDEAEPSTVPGTP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06493-1", "kinase_gene_name": "CDK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ], "site_lbl": "Ser336" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "29254517", "url": "https://glygen.org/publication/PubMed/29254517" } ], "site_lbl": "Ser336" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q99638-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q99638-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q99638-1.326.326", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q99638-1.328.328", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q99638-1.341.341", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q99638-1.355.355", "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": 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": "Q99638-1.355.355", "start_pos": 355, "end_pos": 355, "uniprot_canonical_ac": "Q99638-1", "length": 391, "uniprot_id": "RAD9A_HUMAN", "protein_name": "Cell cycle checkpoint control protein RAD9A", "refseq_ac": "NP_001230153", "refseq_name": "cell cycle checkpoint control protein RAD9A isoform 2", "gene_name": "RAD9A", "gene_names_uniprotkb": "RAD9A", "gene_names_refseq": "RAD9A; RAD9", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A role for the phosphorylation of hRad9 in checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "St Onge RP, Besley BD, Pelley JL, Davey S", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ] }, { "title": "Tousled-like kinase-dependent phosphorylation of Rad9 plays a role in cell cycle progression and G2/M checkpoint exit.", "journal": "PloS one", "date": "2013", "authors": "Kelly R, Davey SK", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "24376897", "url": "https://glygen.org/publication/PubMed/24376897" } ] }, { "title": "Phosphorylation of human Rad9 is required for genotoxin-activated checkpoint signaling.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Roos-Mattjus P, Hopkins KM, Oestreich AJ, Vroman BT, Johnson KL, Naylor S, Lieberman HB, Karnitz LM", "evidence": [ { "database": "UniProtKB", "id": "Q99638", "url": "https://www.uniprot.org/uniprotkb/Q99638" }, { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" } ] }, { "title": "TLK1B mediated phosphorylation of Rad9 regulates its nuclear/cytoplasmic localization and cell cycle checkpoint.", "journal": "BMC molecular biology", "date": "2016", "authors": "Awate S, De Benedetti A", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" } ], "reference": [ { "type": "PubMed", "id": "26860083", "url": "https://glygen.org/publication/PubMed/26860083" } ] } ], "crossref": [ { "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24376897", "url": "https://glygen.org/publication/PubMed/24376897", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26860083", "url": "https://glygen.org/publication/PubMed/26860083", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KSPGPHSEEEDEAEPSTVPG", "down_seq": "PPPKKFRSLFFGSILAPVRS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06493-1", "kinase_gene_name": "CDK1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "12734188", "url": "https://glygen.org/publication/PubMed/12734188" } ], "site_lbl": "Thr355" }, { "kinase_uniprot_canonical_ac": "Q9UKI8-1", "kinase_gene_name": "TLK1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "24376897", "url": "https://glygen.org/publication/PubMed/24376897" } ], "site_lbl": "Thr355" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q99638", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q99638" }, { "database": "PubMed", "id": "12709442", "url": "https://glygen.org/publication/PubMed/12709442" }, { "database": "PubMed", "id": "24376897", "url": "https://glygen.org/publication/PubMed/24376897" }, { "database": "PubMed", "id": "26860083", "url": "https://glygen.org/publication/PubMed/26860083" } ], "site_lbl": "Thr355" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "65", "end_pos": "65" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] }, { "type": "snv", "site_list": [ { "start_pos": "146", "end_pos": "146" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "65", "end_pos": "65" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "266", "end_pos": "266" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "387", "end_pos": "387" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q99638-1.336.336", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q99638-1.341.341", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q99638-1.375.375", "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": 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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O43896-1.1001.1001", "start_pos": 1001, "end_pos": 1001, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "FKSNPQHRESWPGMGSGEAP", "down_seq": "PLQPPEEVTPHPATPARRPP", "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": "Thr1001", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "O43896-1.1010.1010", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O43896-1.1015.1015", "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": 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": "O43896-1.1010.1010", "start_pos": 1010, "end_pos": 1010, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "O43896", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O43896" } ], "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": "O43896", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O43896", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "rs373574368", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373574368", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373574368", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373574368", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373574368", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373574368", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs747596325", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747596325", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747596325", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747596325", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747596325", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747596325#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747596325", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747596325", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SWPGMGSGEAPTPLQPPEEV", "down_seq": "PHPATPARRPPSPRRSHHPR", "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": "Thr1010", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "O43896", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O43896" } ] } ], "snv": [ { "evidence": [ { "id": "rs373574368", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373574368" }, { "id": "rs373574368", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373574368" }, { "id": "rs373574368", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373574368" } ], "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": "17", "chr_pos": "5023867", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1010", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs747596325", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747596325" }, { "id": "rs747596325", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747596325" }, { "id": "rs747596325", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747596325#frequency_tab" }, { "id": "rs747596325", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747596325" } ], "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": "17", "chr_pos": "5023868", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1010", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O43896-1.1001.1001", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O43896-1.1015.1015", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O43896-1.1030.1030", "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": 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": "O43896-1.1015.1015", "start_pos": 1015, "end_pos": 1015, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "rs375145620", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375145620", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs375145620", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375145620#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs375145620", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375145620", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1014528756", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1014528756", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1014528756", "url": "https://www.ensembl.org/id/rs1014528756", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GSGEAPTPLQPPEEVTPHPA", "down_seq": "PARRPPSPRRSHHPRRNSLD", "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": "Thr1015", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs375145620", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375145620" }, { "id": "rs375145620", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375145620#frequency_tab" }, { "id": "rs375145620", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375145620" } ], "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": "17", "chr_pos": "5023883", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1015", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1014528756", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1014528756" }, { "id": "rs1014528756", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1014528756" } ], "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": "17", "chr_pos": "5023882", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1015", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O43896-1.1001.1001", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O43896-1.1010.1010", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O43896-1.1030.1030", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O43896-1.1033.1033", "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": "O43896-1.1030.1030", "start_pos": 1030, "end_pos": 1030, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TPHPATPARRPPSPRRSHHP", "down_seq": "RNSLDGGGRSRGAGSAQPEP", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "5023928", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1030", "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": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O43896-1.1010.1010", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "O43896-1.1015.1015", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O43896-1.1033.1033", "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": "O43896-1.1097.1097", "start_pos": 1097, "end_pos": 1097, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2508223365", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2508223365", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RYPPYTTPPRMRRQRSAPDL", "down_seq": "ESGAAV", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" }, { "id": "rs2508223365", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2508223365" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KES->NES).", "chr_id": "17", "chr_pos": "5024130", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K1097", "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: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": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O43896-1.1082.1082", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "O43896-1.1083.1083", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O43896-1.1092.1092", "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": "O43896-1.13.13", "start_pos": 13, "end_pos": 13, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MAGASVKVAVRV", "down_seq": "PFNARETSQDAKCVVSMQGN", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "5000283", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R13", "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: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": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "O43896-1.18.18", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "O43896-1.163.163", "start_pos": 163, "end_pos": 163, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EVSYMEIYCERVRDLLNPKS", "down_seq": "GSLRVREHPILGPYVQDLSK", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "5002521", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R163", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "O43896-1.180.180", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "O43896-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1382440375", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1382440375", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1382440375", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1382440375", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PKSRGSLRVREHPILGPYVQ", "down_seq": "LSKLAVTSYADIADLMDCGN", "snv": [ { "evidence": [ { "id": "rs1382440375", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1382440375" }, { "id": "rs1382440375", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1382440375" } ], "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": "17", "chr_pos": "5002572", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D180", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O43896-1.163.163", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O43896-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs199632760", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199632760", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199632760", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199632760", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199632760", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199632760", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199632760", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199632760#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199632760", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199632760", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MAGASVKVAVRVRPFNA", "down_seq": "ETSQDAKCVVSMQGNTTSII", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" }, { "id": "rs199632760", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199632760" }, { "id": "rs199632760", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199632760" }, { "id": "rs199632760", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199632760" }, { "id": "rs199632760", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199632760#frequency_tab" }, { "id": "rs199632760", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199632760" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NAR->NAC).", "chr_id": "17", "chr_pos": "5000298", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R18", "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": "rs199632760", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199632760" }, { "id": "rs199632760", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199632760" }, { "id": "rs199632760", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199632760" }, { "id": "rs199632760", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199632760#frequency_tab" }, { "id": "rs199632760", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199632760" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAR->NAS).", "chr_id": "17", "chr_pos": "5000298", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "R18", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "O43896-1.13.13", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "O43896-1.211.211", "start_pos": 211, "end_pos": 211, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748307324", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748307324", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748307324", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748307324", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748307324", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748307324#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748307324", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748307324", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DIADLMDCGNKARTVAATNM", "down_seq": "ETSSRSHAVFTIVFTQRCHD", "snv": [ { "evidence": [ { "id": "rs748307324", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748307324" }, { "id": "rs748307324", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748307324" }, { "id": "rs748307324", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748307324#frequency_tab" }, { "id": "rs748307324", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748307324" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NMN->NMS).", "chr_id": "17", "chr_pos": "5002754", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N211", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "O43896-1.215.215", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O43896-1.215.215", "start_pos": 215, "end_pos": 215, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs199548525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199548525", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199548525", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199548525", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199548525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199548525", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199548525", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199548525#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199548525", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199548525", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LMDCGNKARTVAATNMNETS", "down_seq": "RSHAVFTIVFTQRCHDQLTG", "snv": [ { "evidence": [ { "id": "rs199548525", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199548525" }, { "id": "rs199548525", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199548525" }, { "id": "rs199548525", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199548525" }, { "id": "rs199548525", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199548525#frequency_tab" }, { "id": "rs199548525", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199548525" } ], "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 (SRS->NRS).", "chr_id": "17", "chr_pos": "5002766", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S215", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O43896-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O43896-1.234.234", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O43896-1.234.234", "start_pos": 234, "end_pos": 234, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SSRSHAVFTIVFTQRCHDQL", "down_seq": "GLDSEKVSKISLVDLAGSER", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "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 (3).", "chr_id": "17", "chr_pos": "5002823", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T234", "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": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O43896-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O43896-1.238.238", "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": "O43896-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HAVFTIVFTQRCHDQLTGLD", "down_seq": "EKVSKISLVDLAGSERADSS", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "606", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "5002835", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S238", "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: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": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O43896-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O43896-1.256.256", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "O43896-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs150280414", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150280414", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150280414", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150280414", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs150280414", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150280414", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs150280414", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150280414#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs150280414", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150280414", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LDSEKVSKISLVDLAGSERA", "down_seq": "SSGARGMRLKEGANINKSLT", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" }, { "id": "rs150280414", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150280414" }, { "id": "rs150280414", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150280414" }, { "id": "rs150280414", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150280414" }, { "id": "rs150280414", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150280414#frequency_tab" }, { "id": "rs150280414", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150280414" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "17", "chr_pos": "5003657", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D256", "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:0050941", "recommended_name": { "id": "DOID:0050941", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0050941", "name": "spastic ataxia 2", "description": "A spastic ataxia that is characterized by cerebellar ataxia, spasticity and peripheral neuropathy in the first two decades of life, has_material_basis_in homozygous mutation in the KIF1C gene on chromosome 17p13." }, "synonyms": [ { "id": "MONDO:0012651", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012651", "name": "spastic ataxia 2", "description": "Autosomal recessive spastic paraplegia type 58 is a rare, complex subtype of hereditary spastic paraplegia characterized by variable onset of slowly progressive lower limb spasticity and weakness and prominent cerebellar ataxia, associated with gait disturbances, dysarthria, increased deep tendon reflexes and extensor plantar responses. Additional features may include involuntary movements (i.e. clonus, tremor, fasciculations, chorea), decreased vibration sense, oculomotor abnormalities (e.g. nystagmus) and distal amyotrophy in the upper and lower limbs." }, { "id": "MONDO:0012651", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012651", "name": "KIF1C spastic ataxia", "description": "" }, { "id": "MONDO:0012651", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012651", "name": "SPAX2", "description": "" }, { "id": "MONDO:0012651", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012651", "name": "SPG58", "description": "" }, { "id": "MONDO:0012651", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012651", "name": "autosomal recessive spastic ataxia type 2", "description": "" }, { "id": "MONDO:0012651", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012651", "name": "spastic ataxia 2", "description": "" }, { "id": "MONDO:0012651", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012651", "name": "spastic ataxia caused by mutation in KIF1C", "description": "" }, { "id": "MONDO:0012651", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012651", "name": "spastic ataxia type 2", "description": "" }, { "id": "MONDO:0012651", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012651", "name": "spastic ataxia 2, autosomal recessive", "description": "" }, { "id": "MIM:611302", "resource": "MIM", "url": "https://www.omim.org/entry/611302", "name": "Spastic ataxia 2, autosomal recessive", "description": "Spastic ataxia 2, autosomal recessive" } ], "unlinked_id_list": [], "evidence": [ { "id": "611302", "database": "MIM", "url": "https://www.omim.org/entry/611302" }, { "id": "0050941", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0050941" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O43896-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O43896-1.272.272", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "O43896-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs939497458", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs939497458", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs939497458", "url": "https://www.ncbi.nlm.nih.gov/snp/rs939497458#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs939497458", "url": "http://gnomad.broadinstitute.org/awesome?query=rs939497458", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SERADSSGARGMRLKEGANI", "down_seq": "KSLTTLGKVISALADMQSKK", "snv": [ { "evidence": [ { "id": "rs939497458", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs939497458" }, { "id": "rs939497458", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs939497458#frequency_tab" }, { "id": "rs939497458", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs939497458" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIN->NIS).", "chr_id": "17", "chr_pos": "5003867", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N272", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O43896-1.256.256", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O43896-1.318.318", "start_pos": 318, "end_pos": 318, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs138321138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138321138", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs138321138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138321138", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs138321138", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138321138#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs138321138", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138321138", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IPYRDSVLTWLLKENLGGNS", "down_seq": "TAMIAALSPADINYEETLST", "snv": [ { "evidence": [ { "id": "rs138321138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138321138" }, { "id": "rs138321138", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138321138" }, { "id": "rs138321138", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138321138#frequency_tab" }, { "id": "rs138321138", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138321138" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSR->NSC).", "chr_id": "17", "chr_pos": "5004578", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R318", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs138321138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138321138" }, { "id": "rs138321138", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138321138" }, { "id": "rs138321138", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138321138#frequency_tab" }, { "id": "rs138321138", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138321138" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSR->NSS).", "chr_id": "17", "chr_pos": "5004578", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R318", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "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": "O43896-1.343.343", "start_pos": 343, "end_pos": 343, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1467789736", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1467789736", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1467789736", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1467789736#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1467789736", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1467789736", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AALSPADINYEETLSTLRYA", "down_seq": "RTKQIRCNAIINEDPNARLI", "snv": [ { "evidence": [ { "id": "rs1467789736", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1467789736" }, { "id": "rs1467789736", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1467789736#frequency_tab" }, { "id": "rs1467789736", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1467789736" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DRT->NRT).", "chr_id": "17", "chr_pos": "5004862", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D343", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "O43896-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O43896-1.349.349", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O43896-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ALSPADINYEETLSTLRYAD", "down_seq": "TKQIRCNAIINEDPNARLIR", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "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 (3).", "chr_id": "17", "chr_pos": "5004866", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R344", "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: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": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O43896-1.343.343", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O43896-1.349.349", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "O43896-1.349.349", "start_pos": 349, "end_pos": 349, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DINYEETLSTLRYADRTKQI", "down_seq": "CNAIINEDPNARLIRELQEE", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "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": "17", "chr_pos": "5004880", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R349", "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": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "O43896-1.343.343", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O43896-1.344.344", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "O43896-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778176215", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778176215", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778176215", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778176215", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778176215", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778176215#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778176215", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778176215", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SMQGNTTSIINPKQSKDAPK", "down_seq": "FTFDYSYWSHTSTEDPQFAS", "snv": [ { "evidence": [ { "id": "rs778176215", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778176215" }, { "id": "rs778176215", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778176215" }, { "id": "rs778176215", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778176215#frequency_tab" }, { "id": "rs778176215", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778176215" } ], "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": "17", "chr_pos": "5000811", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S49", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "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": "O43896-1.623.623", "start_pos": 623, "end_pos": 623, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ARLERERGVPPPPGPPSEPV", "down_seq": "WNFAQKELLEQQGIDIKLEM", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "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": "17", "chr_pos": "5020608", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D623", "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" } ] }, { "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": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "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": "O43896-1.678.678", "start_pos": 678, "end_pos": 678, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs551884040", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs551884040", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs551884040", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs551884040", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs551884040", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs551884040", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs551884040", "url": "https://www.ncbi.nlm.nih.gov/snp/rs551884040#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs551884040", "url": "http://gnomad.broadinstitute.org/awesome?query=rs551884040", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KEEADLLLEQQRLYADSDSG", "down_seq": "DSDKRSCEESWRLISSLREQ", "snv": [ { "evidence": [ { "id": "rs551884040", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs551884040" }, { "id": "rs551884040", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs551884040" }, { "id": "rs551884040", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs551884040" }, { "id": "rs551884040", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs551884040#frequency_tab" }, { "id": "rs551884040", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs551884040" } ], "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": "17", "chr_pos": "5022113", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "D678", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O43896-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O43896-1.676.676", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O43896-1.680.680", "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": "O43896-1.864.864", "start_pos": 864, "end_pos": 864, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LQEVKLQNSSKDRELQALRD", "down_seq": "MLRMERVIPLAQDHEDENEE", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "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": "17", "chr_pos": "5022672", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R864", "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: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: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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "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": "O43896-1.896.896", "start_pos": 896, "end_pos": 896, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QDHEDENEEGGEVPWAPPEG", "down_seq": "EAAEEAAPSDRMPSARPPSP", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "17", "chr_pos": "5023526", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S896", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "O43896-1.907.907", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O43896-1.915.915", "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": 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": "O43896-1.907.907", "start_pos": 907, "end_pos": 907, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EVPWAPPEGSEAAEEAAPSD", "down_seq": "MPSARPPSPPLSSWERVSRL", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "5023559", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R907", "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": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O43896-1.896.896", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O43896-1.915.915", "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": "O43896-1.963.963", "start_pos": 963, "end_pos": 963, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O43896", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KQEQLRLQGLQGSGGRGGGL", "down_seq": "RPPARFVPPHDCKLRFPFKS", "snv": [ { "evidence": [ { "id": "O43896", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O43896" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "5023726", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R963", "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: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": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "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": "O43896-1.1033.1033", "start_pos": 1033, "end_pos": 1033, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "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": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "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": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "database": "iPTMnet", "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": "PATPARRPPSPRRSHHPRRN", "down_seq": "LDGGGRSRGAGSAQPEPQHF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1033" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O43896-1.1015.1015", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O43896-1.1030.1030", "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": "O43896-1.1082.1082", "start_pos": 1082, "end_pos": 1082, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PQPPQPYPAQRPPGPRYPPY", "down_seq": "TPPRMRRQRSAPDLKESGAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Thr1082" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "O43896-1.1083.1083", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O43896-1.1092.1092", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O43896-1.1097.1097", "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": "O43896-1.1083.1083", "start_pos": 1083, "end_pos": 1083, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QPPQPYPAQRPPGPRYPPYT", "down_seq": "PPRMRRQRSAPDLKESGAAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Thr1083" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O43896-1.1082.1082", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O43896-1.1092.1092", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O43896-1.1097.1097", "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": "O43896-1.1092.1092", "start_pos": 1092, "end_pos": 1092, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The kinesin-like motor protein KIF1C occurs in intact cells as a dimer and associates with proteins of the 14-3-3 family.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Dorner C, Ullrich A, Haring HU, Lammers R", "evidence": [ { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "10559254", "url": "https://glygen.org/publication/PubMed/10559254" } ] }, { "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] } ], "crossref": [ { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "10559254", "url": "https://glygen.org/publication/PubMed/10559254", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RPPGPRYPPYTTPPRMRRQR", "down_seq": "APDLKESGAAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P19784-1", "kinase_gene_name": "CSNK2A2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" }, { "database": "PubMed", "id": "10559254", "url": "https://glygen.org/publication/PubMed/10559254" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1092" }, { "kinase_uniprot_canonical_ac": "P68400-1", "kinase_gene_name": "CSNK2A1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" }, { "database": "PubMed", "id": "10559254", "url": "https://glygen.org/publication/PubMed/10559254" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1092" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "site_lbl": "Ser1092" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O43896-1.1082.1082", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O43896-1.1083.1083", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O43896-1.1097.1097", "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": 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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O43896-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LTTLGKVISALADMQSKKRK", "down_seq": "DFIPYRDSVLTWLLKENLGG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "site_lbl": "Ser295" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "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": "O43896-1.489.489", "start_pos": 489, "end_pos": 489, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "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": "RMEREALLAEMGVAVREDGG", "down_seq": "VGVFSPKKTPHLVNLNEDPL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr489" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "O43896-1.494.494", "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": "O43896-1.494.494", "start_pos": 494, "end_pos": 494, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] } ], "crossref": [ { "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALLAEMGVAVREDGGTVGVF", "down_seq": "PKKTPHLVNLNEDPLMSECL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "site_lbl": "Ser494" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "O43896-1.489.489", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O43896-1.674.674", "start_pos": 674, "end_pos": 674, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "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": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "database": "iPTMnet", "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": "YRKEKEEADLLLEQQRLYAD", "down_seq": "DSGDDSDKRSCEESWRLISS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser674" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O43896-1.676.676", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O43896-1.678.678", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O43896-1.680.680", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O43896-1.676.676", "start_pos": 676, "end_pos": 676, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "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": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "database": "iPTMnet", "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": "KEKEEADLLLEQQRLYADSD", "down_seq": "GDDSDKRSCEESWRLISSLR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser676" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O43896-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O43896-1.678.678", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O43896-1.680.680", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O43896-1.680.680", "start_pos": 680, "end_pos": 680, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "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": "EADLLLEQQRLYADSDSGDD", "down_seq": "DKRSCEESWRLISSLREQLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser680" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "O43896-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O43896-1.676.676", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O43896-1.678.678", "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": "O43896-1.915.915", "start_pos": 915, "end_pos": 915, "uniprot_canonical_ac": "O43896-1", "length": 1103, "uniprot_id": "KIF1C_HUMAN", "protein_name": "Kinesin-like protein KIF1C", "refseq_ac": "NP_006603", "refseq_name": "kinesin-like protein KIF1C", "gene_name": "KIF1C", "gene_names_uniprotkb": "KIF1C; KIAA0706", "gene_names_refseq": "KIF1C; LTXS1; SATX2; SAX2; SPAX2; SPG58", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" } ], "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896", "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": "GSEAAEEAAPSDRMPSARPP", "down_seq": "PPLSSWERVSRLMEEDPAFR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O43896", "url": "https://www.uniprot.org/uniprotkb/O43896" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O43896", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O43896" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser915" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1001", "end_pos": "1001" }, { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "864", "end_pos": "864" }, { "start_pos": "896", "end_pos": "896" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "963", "end_pos": "963" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1092", "end_pos": "1092" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "915", "end_pos": "915" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O43896-1.896.896", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "O43896-1.907.907", "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": "Q16849-1.441.441", "start_pos": 441, "end_pos": 441, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LC-MS/MS characterization of O-glycosylation sites and glycan structures of human cerebrospinal fluid glycoproteins.", "journal": "Journal of proteome research", "date": "2013", "authors": "Halim A, Ruetschi U, Larson G, Nilsson J", "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849#ptm_processing" }, { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" }, { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "697", "url": "https://glyconnect.expasy.org/browser/proteins/697" } ], "reference": [ { "type": "PubMed", "id": "23234360", "url": "https://glygen.org/publication/PubMed/23234360" } ] }, { "title": "Human urinary glycoproteomics; attachment site specific analysis of N- and O-linked glycosylations by CID and ECD.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Halim A, Nilsson J, Ruetschi U, Hesse C, Larson G", "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849#ptm_processing" }, { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" }, { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "697", "url": "https://glyconnect.expasy.org/browser/proteins/697" } ], "reference": [ { "type": "PubMed", "id": "22171320", "url": "https://glygen.org/publication/PubMed/22171320" } ] } ], "crossref": [ { "id": "23234360", "url": "https://glygen.org/publication/PubMed/23234360", "database": "PubMed", "categories": [ "Other" ] }, { "id": "697", "url": "https://glyconnect.expasy.org/browser/proteins/697", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "22171320", "url": "https://glygen.org/publication/PubMed/22171320", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VQQVPSPVSSEPPKAARPPV", "down_seq": "PVLLEKKSPLGQSQPTVAGQ", "glycosylation": [ { "glytoucan_ac": "G29931IJ", "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": "Thr441", "evidence": [ { "id": "23234360", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23234360" }, { "id": "697", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/697" }, { "id": "22171320", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22171320" } ] }, { "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": "Thr441", "evidence": [ { "id": "22171320", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22171320" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "23234360", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23234360" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr441", "evidence": [ { "id": "Q16849", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q16849#ptm_processing" }, { "id": "23234360", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23234360" }, { "id": "22171320", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22171320" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q16849-1.447.447", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q16849-1.449.449", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q16849-1.454.454", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q16849-1.457.457", "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": 3 }, { "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": 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": 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": 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": "Q16849-1.449.449", "start_pos": 449, "end_pos": 449, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "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": "Q16849", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q16849" } ], "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": "Q16849", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q16849", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "rs752175505", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752175505", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752175505", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752175505", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752175505", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752175505", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSEPPKAARPPVTPVLLEKK", "down_seq": "PLGQSQPTVAGQPSARPAAE", "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": "Ser449", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q16849", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q16849" } ] } ], "snv": [ { "evidence": [ { "id": "rs752175505", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752175505" }, { "id": "rs752175505", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752175505" }, { "id": "rs752175505", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752175505" } ], "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": "219300076", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S449", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q16849-1.441.441", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q16849-1.447.447", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q16849-1.454.454", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q16849-1.457.457", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q16849-1.454.454", "start_pos": 454, "end_pos": 454, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "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": "Q16849", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q16849" } ], "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": "Q16849", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q16849", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KAARPPVTPVLLEKKSPLGQ", "down_seq": "QPTVAGQPSARPAAEEYGYI", "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": "Ser454", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q16849", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q16849" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q16849-1.441.441", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q16849-1.447.447", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q16849-1.449.449", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q16849-1.457.457", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q16849-1.474.474", "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": "Q16849-1.457.457", "start_pos": 457, "end_pos": 457, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "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": "Q16849", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q16849" } ], "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": "Q16849", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q16849", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "rs776149302", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776149302", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776149302", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776149302", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776149302", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776149302#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs776149302", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776149302", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RPPVTPVLLEKKSPLGQSQP", "down_seq": "VAGQPSARPAAEEYGYIVTD", "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": "Thr457", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q16849", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q16849" } ] } ], "snv": [ { "evidence": [ { "id": "rs776149302", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776149302" }, { "id": "rs776149302", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776149302" }, { "id": "rs776149302", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776149302#frequency_tab" }, { "id": "rs776149302", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776149302" } ], "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": "2", "chr_pos": "219300051", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T457", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776149302", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776149302" }, { "id": "rs776149302", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776149302" }, { "id": "rs776149302", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776149302#frequency_tab" }, { "id": "rs776149302", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776149302" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "2", "chr_pos": "219300051", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T457", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->R).", "chr_id": "2", "chr_pos": "219300051", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T457", "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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q16849-1.441.441", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q16849-1.447.447", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q16849-1.449.449", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q16849-1.454.454", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q16849-1.474.474", "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": 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": "Q16849-1.506.506", "start_pos": 506, "end_pos": 506, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Stability of proICA512/IA-2 and its targeting to insulin secretory granules require beta4-sheet-mediated dimerization of its ectodomain in the endoplasmic reticulum.", "journal": "Molecular and cellular biology", "date": "2015", "authors": "Torkko JM, Primo ME, Dirkx R, Friedrich A, Viehrig A, Vergari E, Borgonovo B, Sonmez A, Wegbrod C, Lachnit M, Munster C, Sica MP, Ermacora MR, Solimena M", "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849#ptm_processing" }, { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "reference": [ { "type": "PubMed", "id": "25561468", "url": "https://glygen.org/publication/PubMed/25561468" } ] } ], "crossref": [ { "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25561468", "url": "https://glygen.org/publication/PubMed/25561468", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs776536795", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776536795", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776536795", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776536795", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776536795", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776536795", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GVKLLEILAEHVHMSSGSFI", "down_seq": "ISVVGPALTFRIRHNEQNLS", "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": "Asn506", "evidence": [ { "id": "Q16849", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q16849#ptm_processing" }, { "id": "25561468", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25561468" } ] } ], "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "Reduces N-glycosylation.", "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" }, { "database": "PubMed", "id": "25561468", "url": "https://glygen.org/publication/PubMed/25561468" } ] } ], "snv": [ { "evidence": [ { "id": "rs776536795", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776536795" }, { "id": "rs776536795", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776536795" }, { "id": "rs776536795", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776536795" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIS->IIS).", "chr_id": "2", "chr_pos": "219299706", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N506", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q16849-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q16849-1.517.517", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q16849-1.524.524", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q16849-1.525.525", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q16849-1.526.526", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q16849-1.524.524", "start_pos": 524, "end_pos": 524, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "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": "Stability of proICA512/IA-2 and its targeting to insulin secretory granules require beta4-sheet-mediated dimerization of its ectodomain in the endoplasmic reticulum.", "journal": "Molecular and cellular biology", "date": "2015", "authors": "Torkko JM, Primo ME, Dirkx R, Friedrich A, Viehrig A, Vergari E, Borgonovo B, Sonmez A, Wegbrod C, Lachnit M, Munster C, Sica MP, Ermacora MR, Solimena M", "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849#ptm_processing" }, { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "reference": [ { "type": "PubMed", "id": "25561468", "url": "https://glygen.org/publication/PubMed/25561468" } ] } ], "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": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25561468", "url": "https://glygen.org/publication/PubMed/25561468", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs780890314", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780890314", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780890314", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780890314", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780890314", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780890314#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780890314", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780890314", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FINISVVGPALTFRIRHNEQ", "down_seq": "LSLADVTQQAGLVKSELEAQ", "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": "HNEQnLSLADVTQQAGLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn524", "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": "G15664MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HNEQnLSLADVTQQAGLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn524", "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": "G23719VF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HNEQnLSLADVTQQAGLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn524", "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": "G36379GD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HNEQnLSLADVTQQAGLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn524", "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": "G57317CE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HNEQnLSLADVTQQAGLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn524", "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": "G84349RE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HNEQnLSLADVTQQAGLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn524", "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": "HNEQnLSLADVTQQAGLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn524", "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": "G92275SC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HNEQnLSLADVTQQAGLVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn524", "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": "Asn524", "evidence": [ { "id": "Q16849", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q16849#ptm_processing" }, { "id": "25561468", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25561468" } ] } ], "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "Reduces N-glycosylation.", "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" }, { "database": "PubMed", "id": "25561468", "url": "https://glygen.org/publication/PubMed/25561468" } ] } ], "snv": [ { "evidence": [ { "id": "rs780890314", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780890314" }, { "id": "rs780890314", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780890314" }, { "id": "rs780890314", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780890314#frequency_tab" }, { "id": "rs780890314", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780890314" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->KLS).", "chr_id": "2", "chr_pos": "219299336", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N524", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q16849-1.506.506", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q16849-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q16849-1.517.517", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q16849-1.525.525", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q16849-1.526.526", "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": 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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q16849-1.880.880", "start_pos": 880, "end_pos": 880, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "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": "QTQETRTLTQFHFLSWPAEG", "down_seq": "PASTRPLLDFRRKVNKCYRG", "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": "Thr880", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "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": "Q16849-1.553.553", "start_pos": 553, "end_pos": 553, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Stability of proICA512/IA-2 and its targeting to insulin secretory granules require beta4-sheet-mediated dimerization of its ectodomain in the endoplasmic reticulum.", "journal": "Molecular and cellular biology", "date": "2015", "authors": "Torkko JM, Primo ME, Dirkx R, Friedrich A, Viehrig A, Vergari E, Borgonovo B, Sonmez A, Wegbrod C, Lachnit M, Munster C, Sica MP, Ermacora MR, Solimena M", "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849#ptm_processing" }, { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "reference": [ { "type": "PubMed", "id": "25561468", "url": "https://glygen.org/publication/PubMed/25561468" } ] } ], "crossref": [ { "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25561468", "url": "https://glygen.org/publication/PubMed/25561468", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "QAGLVKSELEAQTGLQILQT", "down_seq": "VGQREEAAAVLPQTAHSTSP", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "D", "comment": "Impairs normal processing and leads to retention in the endoplasmic reticulum and degradation.", "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" }, { "database": "PubMed", "id": "25561468", "url": "https://glygen.org/publication/PubMed/25561468" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "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": "Q16849-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WHDDLTQYVISQEMERIPRL", "down_seq": "PPEPRPRDRSGLAPKRPGPA", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "219303763", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R117", "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: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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "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": "Q16849-1.170.170", "start_pos": 170, "end_pos": 170, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757067162", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757067162", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757067162", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757067162", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757067162", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757067162", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APAAQHRLPQPPVGKGGAGA", "down_seq": "SSLSPLQAELLPPLLEHLLL", "snv": [ { "evidence": [ { "id": "rs757067162", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757067162" }, { "id": "rs757067162", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757067162" }, { "id": "rs757067162", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757067162" } ], "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": "219302706", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S170", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "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": "Q16849-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSPGMVSVGPLPKAEAPALF", "down_seq": "RTASKGIFGDHPGHSYGDLP", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SRT->NRT).", "chr_id": "2", "chr_pos": "219302397", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S245", "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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "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": "Q16849-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs528795949", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs528795949", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs528795949", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs528795949", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs528795949", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs528795949", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs528795949", "url": "http://gnomad.broadinstitute.org/awesome?query=rs528795949", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAQELPAPSRARVPRLPEQG", "down_seq": "SSRAEDSPEGYEKEGLGDRG", "snv": [ { "evidence": [ { "id": "rs528795949", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs528795949" }, { "id": "rs528795949", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs528795949" }, { "id": "rs528795949", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs528795949" }, { "id": "rs528795949", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs528795949" } ], "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": "219302229", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S301", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q16849-1.308.308", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q16849-1.310.310", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q16849-1.310.310", "start_pos": 310, "end_pos": 310, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RARVPRLPEQGSSSRAEDSP", "down_seq": "GYEKEGLGDRGEKPASPAVQ", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "219302201", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E310", "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" } ] }, { "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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q16849-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q16849-1.308.308", "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": "Q16849-1.350.350", "start_pos": 350, "end_pos": 350, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QPDAALQRLAAVLAGYGVEL", "down_seq": "QLTPEQLSTLLTLLQLLPKG", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "219301666", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R350", "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: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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "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": "Q16849-1.386.386", "start_pos": 386, "end_pos": 386, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LLPKGAGRNPGGVVNVGADI", "down_seq": "KTMEGPVEGRDTAELPARTS", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KKT->NKT).", "chr_id": "2", "chr_pos": "219300946", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K386", "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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "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": "Q16849-1.447.447", "start_pos": 447, "end_pos": 447, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1035561939", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1035561939", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1035561939", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1035561939#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1035561939", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1035561939", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PVSSEPPKAARPPVTPVLLE", "down_seq": "KSPLGQSQPTVAGQPSARPA", "snv": [ { "evidence": [ { "id": "rs1035561939", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1035561939" }, { "id": "rs1035561939", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1035561939#frequency_tab" }, { "id": "rs1035561939", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1035561939" } ], "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": "219300080", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K447", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q16849-1.441.441", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q16849-1.449.449", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q16849-1.454.454", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q16849-1.457.457", "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": "Q16849-1.474.474", "start_pos": 474, "end_pos": 474, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747356273", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747356273", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747356273", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747356273", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SQPTVAGQPSARPAAEEYGY", "down_seq": "VTDQKPLSLAAGVKLLEILA", "snv": [ { "evidence": [ { "id": "rs747356273", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747356273" }, { "id": "rs747356273", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747356273" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IVT->NVT).", "chr_id": "2", "chr_pos": "219300000", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I474", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q16849-1.454.454", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q16849-1.457.457", "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": "Q16849-1.508.508", "start_pos": 508, "end_pos": 508, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771067786", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771067786", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771067786", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771067786", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771067786", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771067786#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771067786", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771067786", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KLLEILAEHVHMSSGSFINI", "down_seq": "VVGPALTFRIRHNEQNLSLA", "snv": [ { "evidence": [ { "id": "rs771067786", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771067786" }, { "id": "rs771067786", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771067786" }, { "id": "rs771067786", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771067786#frequency_tab" }, { "id": "rs771067786", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771067786" } ], "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 (NIS->NIN).", "chr_id": "2", "chr_pos": "219299700", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S508", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q16849-1.506.506", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q16849-1.517.517", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q16849-1.524.524", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q16849-1.525.525", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q16849-1.526.526", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q16849-1.517.517", "start_pos": 517, "end_pos": 517, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VHMSSGSFINISVVGPALTF", "down_seq": "IRHNEQNLSLADVTQQAGLV", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "219299358", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R517", "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: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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q16849-1.506.506", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q16849-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q16849-1.524.524", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q16849-1.525.525", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q16849-1.526.526", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q16849-1.525.525", "start_pos": 525, "end_pos": 525, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1342977180", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1342977180", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1342977180", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1342977180", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "INISVVGPALTFRIRHNEQN", "down_seq": "SLADVTQQAGLVKSELEAQT", "snv": [ { "evidence": [ { "id": "rs1342977180", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1342977180" }, { "id": "rs1342977180", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1342977180" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->NPS).", "chr_id": "2", "chr_pos": "219299334", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L525", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q16849-1.506.506", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q16849-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q16849-1.517.517", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q16849-1.524.524", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q16849-1.526.526", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q16849-1.526.526", "start_pos": 526, "end_pos": 526, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs921589581", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs921589581", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs921589581", "url": "https://www.ncbi.nlm.nih.gov/snp/rs921589581#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NISVVGPALTFRIRHNEQNL", "down_seq": "LADVTQQAGLVKSELEAQTG", "snv": [ { "evidence": [ { "id": "rs921589581", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs921589581" }, { "id": "rs921589581", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs921589581#frequency_tab" } ], "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 (NLS->NLF).", "chr_id": "2", "chr_pos": "219299331", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S526", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q16849-1.506.506", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q16849-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q16849-1.517.517", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q16849-1.524.524", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q16849-1.525.525", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q16849-1.601.601", "start_pos": 601, "end_pos": 601, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LVALAGVAGLLVALAVALCV", "down_seq": "QHARQQDKERLAALGPEGAH", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "2", "chr_pos": "219297970", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R601", "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: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" ] }, { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "2", "chr_pos": "219297971", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R601", "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: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" } ] }, { "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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "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": "Q16849-1.623.623", "start_pos": 623, "end_pos": 623, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1952240662", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1952240662", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1952240662", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1952240662#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1952240662", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1952240662", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HARQQDKERLAALGPEGAHG", "down_seq": "TTFEYQDLCRQHMATKSLFN", "snv": [ { "evidence": [ { "id": "rs1952240662", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1952240662" }, { "id": "rs1952240662", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1952240662#frequency_tab" }, { "id": "rs1952240662", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1952240662" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DTT->NTT).", "chr_id": "2", "chr_pos": "219297905", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D623", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q16849-1.630.630", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q16849-1.630.630", "start_pos": 630, "end_pos": 630, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs373382338", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373382338", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ERLAALGPEGAHGDTTFEYQ", "down_seq": "LCRQHMATKSLFNRAEGPPE", "snv": [ { "evidence": [ { "id": "rs373382338", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373382338" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLC->NLC).", "chr_id": "2", "chr_pos": "219297433", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D630", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q16849-1.623.623", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q16849-1.645.645", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q16849-1.645.645", "start_pos": 645, "end_pos": 645, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774512131", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774512131", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774512131", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774512131", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774512131", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774512131", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TFEYQDLCRQHMATKSLFNR", "down_seq": "EGPPEPSRVSSVSSQFSDAA", "snv": [ { "evidence": [ { "id": "rs774512131", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774512131" }, { "id": "rs774512131", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774512131" }, { "id": "rs774512131", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774512131" } ], "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": "219297388", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A645", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q16849-1.630.630", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q16849-1.656.656", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q16849-1.656.656", "start_pos": 656, "end_pos": 656, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1289275256", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289275256", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1289275256", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1289275256#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1289275256", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1289275256", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MATKSLFNRAEGPPEPSRVS", "down_seq": "VSSQFSDAAQASPSSHSSTP", "snv": [ { "evidence": [ { "id": "rs1289275256", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289275256" }, { "id": "rs1289275256", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1289275256#frequency_tab" }, { "id": "rs1289275256", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1289275256" } ], "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": "2", "chr_pos": "219297354", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S656", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q16849-1.645.645", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q16849-1.672.672", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q16849-1.673.673", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q16849-1.672.672", "start_pos": 672, "end_pos": 672, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SRVSSVSSQFSDAAQASPSS", "down_seq": "SSTPSWCEEPAQANMDISTG", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "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 (HSS->NSS).", "chr_id": "2", "chr_pos": "219297307", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H672", "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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q16849-1.656.656", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q16849-1.673.673", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q16849-1.686.686", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q16849-1.688.688", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q16849-1.673.673", "start_pos": 673, "end_pos": 673, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RVSSVSSQFSDAAQASPSSH", "down_seq": "STPSWCEEPAQANMDISTGH", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [ "n-glyco-sequon-gain", "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: n-glyco-sequon-gain (SST->NST).", "chr_id": "2", "chr_pos": "219297303", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S673", "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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q16849-1.656.656", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q16849-1.672.672", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q16849-1.686.686", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q16849-1.688.688", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q16849-1.686.686", "start_pos": 686, "end_pos": 686, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QASPSSHSSTPSWCEEPAQA", "down_seq": "MDISTGHMILAYMEDHLRNR", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "219297264", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N686", "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": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q16849-1.672.672", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q16849-1.673.673", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q16849-1.688.688", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q16849-1.688.688", "start_pos": 688, "end_pos": 688, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs142270672", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142270672", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142270672", "url": "https://www.ensembl.org/id/rs142270672", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs142270672", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142270672", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SPSSHSSTPSWCEEPAQANM", "down_seq": "ISTGHMILAYMEDHLRNRDR", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" }, { "id": "rs142270672", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142270672" }, { "id": "rs142270672", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs142270672" }, { "id": "rs142270672", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142270672" } ], "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 (DIS->NIS).", "chr_id": "2", "chr_pos": "219297259", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D688", "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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q16849-1.672.672", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q16849-1.673.673", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q16849-1.686.686", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q16849-1.801.801", "start_pos": 801, "end_pos": 801, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs973722618", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs973722618", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs973722618", "url": "https://www.ncbi.nlm.nih.gov/snp/rs973722618#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IATQGPLSHTIADFWQMVWE", "down_seq": "GCTVIVMLTPLVEDGVKQCD", "snv": [ { "evidence": [ { "id": "rs973722618", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs973722618" }, { "id": "rs973722618", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs973722618#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 (SGC->NGC).", "chr_id": "2", "chr_pos": "219296332", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S801", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "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": "Q16849-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CQVGVGQARPLLQVTSPVLQ", "down_seq": "LQGVLRQLMSQGLSWHDDLT", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "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": "2", "chr_pos": "219307480", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R82", "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: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: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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q16849-1.91.91", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q16849-1.913.913", "start_pos": 913, "end_pos": 913, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KVNKCYRGRSCPIIVHCSDG", "down_seq": "GRTGTYILIDMVLNRMAKGV", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "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": "2", "chr_pos": "219290882", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A913", "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": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q16849-1.929.929", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q16849-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "PLLQVTSPVLQRLQGVLRQL", "down_seq": "SQGLSWHDDLTQYVISQEME", "snv": [ { "evidence": [ { "id": "Q16849", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q16849" } ], "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": "2", "chr_pos": "219307452", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "M91", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q16849-1.82.82", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q16849-1.929.929", "start_pos": 929, "end_pos": 929, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1477850283", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1477850283", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1477850283", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1477850283#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1477850283", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1477850283", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "CSDGAGRTGTYILIDMVLNR", "down_seq": "AKGVKEIDIAATLEHVRDQR", "snv": [ { "evidence": [ { "id": "rs1477850283", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1477850283" }, { "id": "rs1477850283", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1477850283#frequency_tab" }, { "id": "rs1477850283", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1477850283" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRM->NRT).", "chr_id": "2", "chr_pos": "219290834", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M929", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q16849-1.913.913", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q16849-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "Q16849-1", "length": 979, "uniprot_id": "PTPRN_HUMAN", "protein_name": "Receptor-type tyrosine-protein phosphatase-like N", "refseq_ac": "NP_001186692", "refseq_name": "receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor", "gene_name": "PTPRN", "gene_names_uniprotkb": "PTPRN; ICA3; ICA512", "gene_names_refseq": "IA-2/PTP; IA-2; IA2; ICA512; PTPRN; R-PTP-N", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSRARVPRLPEQGSSSRAED", "down_seq": "PEGYEKEGLGDRGEKPASPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q16849", "url": "https://www.uniprot.org/uniprotkb/Q16849" } ], "site_lbl": "Ser308" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "441", "end_pos": "441" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "880", "end_pos": "880" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "506", "end_pos": "506" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "553", "end_pos": "553" } ] }, { "type": "snv", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "645", "end_pos": "645" }, { "start_pos": "656", "end_pos": "656" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "801", "end_pos": "801" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "913", "end_pos": "913" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q16849-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q16849-1.310.310", "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": "P10620-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P10620-1", "length": 155, "uniprot_id": "MGST1_HUMAN", "protein_name": "Microsomal glutathione S-transferase 1", "refseq_ac": "NP_001247440", "refseq_name": "microsomal glutathione S-transferase 1 isoform a", "gene_name": "MGST1", "gene_names_uniprotkb": "MGST1; GST12; MGST", "gene_names_refseq": "GST12; MGST-I; MGST1; MGST; PMAN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P10620", "url": "https://www.uniprot.org/uniprotkb/P10620" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAcylation promotes fatty acid synthase activity under nutritional stress as a pro-survival mechanism in cancer cells.", "journal": "Proteomics", "date": "2022", "authors": "Wong YK, Wang J, Lim TK, Lin Q, Yap CT, Shen HM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P10620", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P10620" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "P10620", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P10620" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "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": "P10620", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P10620" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] } ], "crossref": [ { "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P10620", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P10620", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "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": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "P10620", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P10620" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "64", "end_pos": "64" }, { "start_pos": "73", "end_pos": "73" } ] } ], "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P10620-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "P10620-1", "length": 155, "uniprot_id": "MGST1_HUMAN", "protein_name": "Microsomal glutathione S-transferase 1", "refseq_ac": "NP_001247440", "refseq_name": "microsomal glutathione S-transferase 1 isoform a", "gene_name": "MGST1", "gene_names_uniprotkb": "MGST1; GST12; MGST", "gene_names_refseq": "GST12; MGST-I; MGST1; MGST; PMAN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P10620", "url": "https://www.uniprot.org/uniprotkb/P10620" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P10620", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P10620", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FANPEDCVAFGKGENAKKYL", "down_seq": "TDDRVERVRRAHLNDLENII", "snv": [ { "evidence": [ { "id": "P10620", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P10620" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "5", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "12", "chr_pos": "16357669", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R64", "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: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: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": "snv", "site_list": [ { "start_pos": "64", "end_pos": "64" }, { "start_pos": "73", "end_pos": "73" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P10620-1.73.73", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "P10620-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "P10620-1", "length": 155, "uniprot_id": "MGST1_HUMAN", "protein_name": "Microsomal glutathione S-transferase 1", "refseq_ac": "NP_001247440", "refseq_name": "microsomal glutathione S-transferase 1 isoform a", "gene_name": "MGST1", "gene_names_uniprotkb": "MGST1; GST12; MGST", "gene_names_refseq": "GST12; MGST-I; MGST1; MGST; PMAN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P10620", "url": "https://www.uniprot.org/uniprotkb/P10620" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P10620", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P10620", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FGKGENAKKYLRTDDRVERV", "down_seq": "RAHLNDLENIIPFLGIGLLY", "snv": [ { "evidence": [ { "id": "P10620", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P10620" } ], "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": "12", "chr_pos": "16357696", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R73", "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: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": "64", "end_pos": "64" }, { "start_pos": "73", "end_pos": "73" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P10620-1.64.64", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8IUZ0-1.138.138", "start_pos": 138, "end_pos": 138, "uniprot_canonical_ac": "Q8IUZ0-1", "length": 686, "uniprot_id": "LRC49_HUMAN", "protein_name": "Leucine-rich repeat-containing protein 49", "refseq_ac": "NP_001185946", "refseq_name": "leucine-rich repeat-containing protein 49 isoform 1", "gene_name": "LRRC49", "gene_names_uniprotkb": "LRRC49; CSTPP2", "gene_names_refseq": "CSTPP2; LRRC49; PGs4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IUZ0", "url": "https://www.uniprot.org/uniprotkb/Q8IUZ0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IUZ0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IUZ0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NFQHNFITRIQNISNLQKLI", "down_seq": "LDLYDNQIEEISGLSTLRCL", "snv": [ { "evidence": [ { "id": "Q8IUZ0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IUZ0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "70904668", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S138", "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": "138", "end_pos": "138" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "669", "end_pos": "669" } ] } ], "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": "Q8IUZ0-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "Q8IUZ0-1", "length": 686, "uniprot_id": "LRC49_HUMAN", "protein_name": "Leucine-rich repeat-containing protein 49", "refseq_ac": "NP_001185946", "refseq_name": "leucine-rich repeat-containing protein 49 isoform 1", "gene_name": "LRRC49", "gene_names_uniprotkb": "LRRC49; CSTPP2", "gene_names_refseq": "CSTPP2; LRRC49; PGs4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IUZ0", "url": "https://www.uniprot.org/uniprotkb/Q8IUZ0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IUZ0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IUZ0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "NLNGLDSLTELNLRHNQITF", "down_seq": "RDVDNLPCLQHLFLSFNNIS", "snv": [ { "evidence": [ { "id": "Q8IUZ0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IUZ0" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "70919191", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V237", "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: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: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": "138", "end_pos": "138" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "669", "end_pos": "669" } ] } ], "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": "Q8IUZ0-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "Q8IUZ0-1", "length": 686, "uniprot_id": "LRC49_HUMAN", "protein_name": "Leucine-rich repeat-containing protein 49", "refseq_ac": "NP_001185946", "refseq_name": "leucine-rich repeat-containing protein 49 isoform 1", "gene_name": "LRRC49", "gene_names_uniprotkb": "LRRC49; CSTPP2", "gene_names_refseq": "CSTPP2; LRRC49; PGs4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IUZ0", "url": "https://www.uniprot.org/uniprotkb/Q8IUZ0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IUZ0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IUZ0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IQTSSLPEKNKVEFKLNKDT", "down_seq": "SFPGRLLQHDLERNYSSRQG", "snv": [ { "evidence": [ { "id": "Q8IUZ0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IUZ0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "70895877", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S45", "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": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "669", "end_pos": "669" } ] } ], "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": "Q8IUZ0-1.588.588", "start_pos": 588, "end_pos": 588, "uniprot_canonical_ac": "Q8IUZ0-1", "length": 686, "uniprot_id": "LRC49_HUMAN", "protein_name": "Leucine-rich repeat-containing protein 49", "refseq_ac": "NP_001185946", "refseq_name": "leucine-rich repeat-containing protein 49 isoform 1", "gene_name": "LRRC49", "gene_names_uniprotkb": "LRRC49; CSTPP2", "gene_names_refseq": "CSTPP2; LRRC49; PGs4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IUZ0", "url": "https://www.uniprot.org/uniprotkb/Q8IUZ0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IUZ0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IUZ0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RKKQFRYLLESKGKKPGIIN", "down_seq": "ENNDSKRLVGENTNRATLNY", "snv": [ { "evidence": [ { "id": "Q8IUZ0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IUZ0" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "71037237", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E588", "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": "138", "end_pos": "138" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "669", "end_pos": "669" } ] } ], "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": "Q8IUZ0-1.669.669", "start_pos": 669, "end_pos": 669, "uniprot_canonical_ac": "Q8IUZ0-1", "length": 686, "uniprot_id": "LRC49_HUMAN", "protein_name": "Leucine-rich repeat-containing protein 49", "refseq_ac": "NP_001185946", "refseq_name": "leucine-rich repeat-containing protein 49 isoform 1", "gene_name": "LRRC49", "gene_names_uniprotkb": "LRRC49; CSTPP2", "gene_names_refseq": "CSTPP2; LRRC49; PGs4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IUZ0", "url": "https://www.uniprot.org/uniprotkb/Q8IUZ0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IUZ0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IUZ0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LQKLWPQMFIELVRDAVIEI", "down_seq": "NKNSYMKLCLQQITDQK", "snv": [ { "evidence": [ { "id": "Q8IUZ0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IUZ0" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "15", "chr_pos": "71049556", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R669", "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: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: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": "138", "end_pos": "138" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "669", "end_pos": "669" } ] } ], "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": "A5PL33-1.689.689", "start_pos": 689, "end_pos": 689, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "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": "rs774652650", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774652650", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774652650", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774652650", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774652650", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774652650#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774652650", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774652650", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ERDRLPSCKPPVPLSPCPGG", "down_seq": "PAGSSGGSPGEDPRRTEPRY", "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": "Thr689", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs774652650", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774652650" }, { "id": "rs774652650", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774652650" }, { "id": "rs774652650", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774652650#frequency_tab" }, { "id": "rs774652650", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774652650" } ], "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": "7", "chr_pos": "149730488", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T689", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774652650", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774652650" }, { "id": "rs774652650", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774652650" }, { "id": "rs774652650", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774652650#frequency_tab" }, { "id": "rs774652650", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774652650" } ], "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": "7", "chr_pos": "149730488", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T689", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "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" ] }, { "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": "A5PL33-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A5PL33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs537244893", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs537244893", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs537244893", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs537244893", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs537244893", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs537244893", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs537244893", "url": "https://www.ncbi.nlm.nih.gov/snp/rs537244893#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs537244893", "url": "http://gnomad.broadinstitute.org/awesome?query=rs537244893", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs537244893", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs537244893", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LLSCLPDGPTSQPHLATTPT", "down_seq": "SSCSSGPTGDGVQGSPLPIK", "snv": [ { "evidence": [ { "id": "A5PL33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33" }, { "id": "rs537244893", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs537244893" }, { "id": "rs537244893", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs537244893" }, { "id": "rs537244893", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs537244893" }, { "id": "rs537244893", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs537244893#frequency_tab" }, { "id": "rs537244893", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs537244893" }, { "id": "rs537244893", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs537244893" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "7", "chr_pos": "149721475", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D136", "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": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "A5PL33-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "A5PL33-1.154.154", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "A5PL33-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs879242300", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs879242300", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs879242300", "url": "http://gnomad.broadinstitute.org/awesome?query=rs879242300", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSCLPDGPTSQPHLATTPTD", "down_seq": "SCSSGPTGDGVQGSPLPIKT", "snv": [ { "evidence": [ { "id": "rs879242300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs879242300" }, { "id": "rs879242300", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs879242300" } ], "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 (SSC->NSC).", "chr_id": "7", "chr_pos": "149721479", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S137", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "A5PL33-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "A5PL33-1.154.154", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A5PL33-1.154.154", "start_pos": 154, "end_pos": 154, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A5PL33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PTDSSCSSGPTGDGVQGSPL", "down_seq": "IKTADKPWPTRKEGPGALGG", "snv": [ { "evidence": [ { "id": "A5PL33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33" } ], "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 (3).", "chr_id": "7", "chr_pos": "149721529", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P154", "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": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "A5PL33-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "A5PL33-1.137.137", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "A5PL33-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A5PL33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CLKELPEAQDRHPSPSGVGN", "down_seq": "RLQENPGAWKRGSGGPGYLL", "snv": [ { "evidence": [ { "id": "A5PL33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33" } ], "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 (4).", "chr_id": "7", "chr_pos": "149723845", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R295", "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: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": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "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": "A5PL33-1.399.399", "start_pos": 399, "end_pos": 399, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A5PL33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASSSPLEALEACLKGIPPNG", "down_seq": "SPSQLPPTSCSQNPQPGDSR", "snv": [ { "evidence": [ { "id": "A5PL33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33" } ], "glycoeffect": [ "n-glyco-sequon-loss", "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": "7", "chr_pos": "149725384", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S399", "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: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": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "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": "A5PL33-1.486.486", "start_pos": 486, "end_pos": 486, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1798083806", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1798083806", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1798083806", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1798083806", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "FSSSSSTDWDLDFGSPVGNQ", "down_seq": "QHPGKGSPPGSSPLQGLENC", "snv": [ { "evidence": [ { "id": "rs1798083806", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1798083806" }, { "id": "rs1798083806", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1798083806" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NQG->NQS).", "chr_id": "7", "chr_pos": "149725940", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G486", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "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": "A5PL33-1.550.550", "start_pos": 550, "end_pos": 550, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A5PL33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RRAEPRNWTADKEGLRAEAC", "down_seq": "SARLGQGRGEAPTRSLHLVS", "snv": [ { "evidence": [ { "id": "A5PL33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "149729208", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E550", "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: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": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "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": "A5PL33-1.616.616", "start_pos": 616, "end_pos": 616, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A5PL33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GVWRWLPEGSAPKPSPLHCL", "down_seq": "SALRGILPVRPLRFACVGGP", "snv": [ { "evidence": [ { "id": "A5PL33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "E", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "7", "chr_pos": "149730182", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E616", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "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": "A5PL33-1.88.88", "start_pos": 88, "end_pos": 88, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1044530330", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1044530330", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1044530330", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1044530330#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1044530330", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1044530330", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VKEIPEFLFGEVKGAMDSPE", "down_seq": "ESRGASLDGERASPEAAAAR", "snv": [ { "evidence": [ { "id": "rs1044530330", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1044530330" }, { "id": "rs1044530330", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1044530330#frequency_tab" }, { "id": "rs1044530330", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1044530330" } ], "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": "7", "chr_pos": "149720943", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S88", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "A5PL33-1.101.101", "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": "A5PL33-1.929.929", "start_pos": 929, "end_pos": 929, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A5PL33", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1798617312", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1798617312", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1798617312", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1798617312", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RRARPLPPDAPPAEPPGLHC", "down_seq": "SSQQLLSSTPSCHAAPPAHP", "snv": [ { "evidence": [ { "id": "A5PL33", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A5PL33" }, { "id": "rs1798617312", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1798617312" }, { "id": "rs1798617312", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1798617312" } ], "glycoeffect": [ "n-glyco-sequon-gain", "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: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "7", "chr_pos": "149733740", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S929", "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": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "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": "A5PL33-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "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": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAMDSPESESRGASLDGERA", "down_seq": "PEAAAAREPCPLRGLLSCLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "site_lbl": "Ser101" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "A5PL33-1.88.88", "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": "A5PL33-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "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": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TADKPWPTRKEGPGALGGEP", "down_seq": "PPTHSPSRRKSHRGQERGTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "site_lbl": "Ser177" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "A5PL33-1.182.182", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "A5PL33-1.184.184", "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": "A5PL33-1.182.182", "start_pos": 182, "end_pos": 182, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "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": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WPTRKEGPGALGGEPSPPTH", "down_seq": "PSRRKSHRGQERGTSEAGIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "site_lbl": "Ser182" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "A5PL33-1.177.177", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "A5PL33-1.184.184", "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": "A5PL33-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "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": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TRKEGPGALGGEPSPPTHSP", "down_seq": "RRKSHRGQERGTSEAGISPG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "site_lbl": "Ser184" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "A5PL33-1.177.177", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "A5PL33-1.182.182", "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": "A5PL33-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "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": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QGLINCLKEILVPGPRHPET", "down_seq": "PSFLPPLPSLGTSRLTRADL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "site_lbl": "Ser229" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "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": "A5PL33-1.253.253", "start_pos": 253, "end_pos": 253, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "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": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "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": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "A5PL33-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPPLPSLGTSRLTRADLGPG", "down_seq": "PPWAVKTEAVSGDCPLQGLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "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": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Ser253" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A5PL33-1.355.355", "start_pos": 355, "end_pos": 355, "uniprot_canonical_ac": "A5PL33-1", "length": 1030, "uniprot_id": "KRBD3_HUMAN", "protein_name": "KRAB domain-containing protein 3", "refseq_ac": "NP_001277116", "refseq_name": "KRAB domain-containing protein 3 isoform 2", "gene_name": "KRABD3", "gene_names_uniprotkb": "KRABD3; KIAA1862; KRBA1", "gene_names_refseq": "KRABD3; KRBA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" } ], "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": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSWVQSPPGPASCQPGRQPL", "down_seq": "PSATGDTRGVPQPSWGPEAQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A5PL33", "url": "https://www.uniprot.org/uniprotkb/A5PL33" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "A5PL33", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A5PL33" } ], "site_lbl": "Ser355" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "689", "end_pos": "689" } ] }, { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "550", "end_pos": "550" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "689", "end_pos": "689" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "929", "end_pos": "929" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "355", "end_pos": "355" } ] } ], "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": "Q9Y448-1.56.56", "start_pos": 56, "end_pos": 56, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "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": "2078", "url": "https://glyconnect.expasy.org/browser/proteins/2078" } ], "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": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "2078", "url": "https://glyconnect.expasy.org/browser/proteins/2078", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "rs201825411", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201825411", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201825411", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201825411", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201825411", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201825411", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201825411", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201825411#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201825411", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201825411", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs201825411", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201825411", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FETQAADLAGGTTVAAGNLL", "down_seq": "ESEKDCGQDRRAPGVQPCRL", "glycosylation": [ { "glytoucan_ac": "G08293MJ", "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": "Asn56", "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": "G84452RH", "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": "Asn56", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "2078", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2078" } ] } ], "snv": [ { "evidence": [ { "id": "rs201825411", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201825411" }, { "id": "rs201825411", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201825411" }, { "id": "rs201825411", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201825411" }, { "id": "rs201825411", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201825411#frequency_tab" }, { "id": "rs201825411", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201825411" }, { "id": "rs201825411", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201825411" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NES->KES).", "chr_id": "15", "chr_pos": "40383003", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N56", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q9Y448-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9Y448-1.58.58", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q9Y448-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PEAPPLDRVFRTTWLSTECD", "down_seq": "HPLPPSYRKFLFETQAADLA", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "45", "frequency": "2.2", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 2 filters: patient freq. (2.2%); patient count (45/2053).", "chr_id": "15", "chr_pos": "40382906", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S24", "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": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9Y448-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9Y448-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9Y448-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9Y448-1.23.23", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q9Y448-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MAAPEAPPLD", "down_seq": "VFRTTWLSTECDSHPLPPSY", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "10", "frequency": "0.5", "sequence_org": "R", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: patient count (10/2053).", "chr_id": "15", "chr_pos": "40382867", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R11", "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": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9Y448-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9Y448-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9Y448-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9Y448-1.24.24", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q9Y448-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs761636030", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761636030", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761636030", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761636030", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761636030", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761636030#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs761636030", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761636030", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs761636030", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs761636030", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ADTQTRATSKSLLPVRSKEV", "down_seq": "VSKQLHSGGPENDVTKITKL", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" }, { "id": "rs761636030", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761636030" }, { "id": "rs761636030", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761636030" }, { "id": "rs761636030", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761636030#frequency_tab" }, { "id": "rs761636030", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761636030" }, { "id": "rs761636030", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs761636030" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DVS->NVS).", "chr_id": "15", "chr_pos": "40386418", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D121", "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: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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q9Y448-1.128.128", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9Y448-1.134.134", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9Y448-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MAAPEAPPLDR", "down_seq": "FRTTWLSTECDSHPLPPSYR", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "V", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "15", "chr_pos": "40382870", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "V12", "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: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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9Y448-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9Y448-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9Y448-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9Y448-1.24.24", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q9Y448-1.134.134", "start_pos": 134, "end_pos": 134, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs887498544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887498544", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs887498544", "url": "https://www.ensembl.org/id/rs887498544", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs887498544", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs887498544", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PVRSKEVDVSKQLHSGGPEN", "down_seq": "VTKITKLRRENGQMKATDTA", "snv": [ { "evidence": [ { "id": "rs887498544", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887498544" }, { "id": "rs887498544", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs887498544" }, { "id": "rs887498544", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs887498544" } ], "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": "15", "chr_pos": "40386457", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D134", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q9Y448-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9Y448-1.128.128", "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": "Q9Y448-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KLRRENGQMKATDTATRRNV", "down_seq": "KGYKPLSKQKSEEELKDKNQ", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NVR->NVT).", "chr_id": "15", "chr_pos": "40387200", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "R160", "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": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q9Y448-1.171.171", "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": "Q9Y448-1.194.194", "start_pos": 194, "end_pos": 194, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779872269", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779872269", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779872269", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779872269", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779872269", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779872269#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779872269", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779872269", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ELKDKNQLLEAVNKQLHQKL", "down_seq": "ETQGELKDLTQKVELLEKFR", "snv": [ { "evidence": [ { "id": "rs779872269", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779872269" }, { "id": "rs779872269", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779872269" }, { "id": "rs779872269", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779872269#frequency_tab" }, { "id": "rs779872269", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779872269" } ], "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 (TET->NET).", "chr_id": "15", "chr_pos": "40389601", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T194", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q9Y448-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9Y448-1.214.214", "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": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9Y448-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LEAVNKQLHQKLTETQGELK", "down_seq": "LTQKVELLEKFRDNCLAILE", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" } ], "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 (DLT->NLT).", "chr_id": "15", "chr_pos": "40389848", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D202", "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": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9Y448-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9Y448-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9Y448-1.218.218", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9Y448-1.214.214", "start_pos": 214, "end_pos": 214, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TETQGELKDLTQKVELLEKF", "down_seq": "DNCLAILESKGLDPALGSET", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" } ], "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 (3).", "chr_id": "15", "chr_pos": "40389884", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R214", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9Y448-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9Y448-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9Y448-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9Y448-1.232.232", "categories": [ "snv_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": "Q9Y448-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs191518976", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs191518976", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs191518976", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs191518976", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs191518976", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs191518976", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs191518976", "url": "https://www.ncbi.nlm.nih.gov/snp/rs191518976#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs191518976", "url": "http://gnomad.broadinstitute.org/awesome?query=rs191518976", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "GELKDLTQKVELLEKFRDNC", "down_seq": "AILESKGLDPALGSETLASR", "snv": [ { "evidence": [ { "id": "rs191518976", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs191518976" }, { "id": "rs191518976", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs191518976" }, { "id": "rs191518976", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs191518976" }, { "id": "rs191518976", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs191518976#frequency_tab" }, { "id": "rs191518976", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs191518976" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCL->NCS).", "chr_id": "15", "chr_pos": "40389897", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "L218", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9Y448-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9Y448-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9Y448-1.232.232", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9Y448-1.237.237", "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": "Q9Y448-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of SKAP by GSK3beta ensures chromosome segregation by a temporal inhibition of Kif2b activity.", "journal": "Scientific reports", "date": "2016", "authors": "Qin B, Cao D, Wu H, Mo F, Shao H, Chu J, Powell M, Aikhionbare F, Wang D, Fu C, He P, Pan W, Wang W, Liu X, Yao X", "evidence": [ { "database": "iPTMnet", "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448" } ], "reference": [ { "type": "PubMed", "id": "27982129", "url": "https://glygen.org/publication/PubMed/27982129" } ] } ], "crossref": [ { "id": "rs1889995880", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1889995880", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1889995880", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1889995880#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1889995880", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1889995880", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "27982129", "url": "https://glygen.org/publication/PubMed/27982129", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KFRDNCLAILESKGLDPALG", "down_seq": "ETLASRQESTTDHMDSMLLL", "snv": [ { "evidence": [ { "id": "rs1889995880", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1889995880" }, { "id": "rs1889995880", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1889995880#frequency_tab" }, { "id": "rs1889995880", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1889995880" } ], "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 (SET->NET).", "chr_id": "15", "chr_pos": "40391502", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S232", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448" }, { "database": "PubMed", "id": "27982129", "url": "https://glygen.org/publication/PubMed/27982129" } ], "site_lbl": "Ser232" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9Y448-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9Y448-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9Y448-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9Y448-1.248.248", "categories": [ "phosphorylation_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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "Q9Y448-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "APEAPPLDRVFRTTWLSTEC", "down_seq": "SHPLPPSYRKFLFETQAADL", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "40382902", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D23", "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: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": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9Y448-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9Y448-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9Y448-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9Y448-1.24.24", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q9Y448-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DHMDSMLLLETLQEELKLFN", "down_seq": "TAKKQMEELQALKVKLEMKE", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" } ], "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 (4).", "chr_id": "15", "chr_pos": "40391991", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E264", "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: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": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9Y448-1.248.248", "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": "Q9Y448-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LFETQAADLAGGTTVAAGNL", "down_seq": "NESEKDCGQDRRAPGVQPCR", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLL->NLS).", "chr_id": "15", "chr_pos": "40382999", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L55", "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": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q9Y448-1.56.56", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9Y448-1.58.58", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q9Y448-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs946109132", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs946109132", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs946109132", "url": "https://www.ensembl.org/id/rs946109132", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TQAADLAGGTTVAAGNLLNE", "down_seq": "EKDCGQDRRAPGVQPCRLVT", "snv": [ { "evidence": [ { "id": "rs946109132", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs946109132" }, { "id": "rs946109132", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs946109132" } ], "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 (NES->NER).", "chr_id": "15", "chr_pos": "40383007", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S58", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q9Y448-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9Y448-1.56.56", "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": "Q9Y448-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9Y448", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MAAP", "down_seq": "APPLDRVFRTTWLSTECDSH", "snv": [ { "evidence": [ { "id": "Q9Y448", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9Y448" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "5", "frequency": "0.2", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "15", "chr_pos": "40382848", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E5", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q9Y448-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9Y448-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9Y448-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9Y448-1.24.24", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q9Y448-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Molecular cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" }, { "database": "iPTMnet", "id": "Q9Y448-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TSKSLLPVRSKEVDVSKQLH", "down_seq": "GGPENDVTKITKLRRENGQM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "iPTMnet", "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448" } ], "site_lbl": "Ser128" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9Y448-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9Y448-1.134.134", "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": "Q9Y448-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "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": "Q9Y448-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448", "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": "TDTATRRNVRKGYKPLSKQK", "down_seq": "EEELKDKNQLLEAVNKQLHQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser171" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9Y448-1.160.160", "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": "Q9Y448-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of SKAP by GSK3beta ensures chromosome segregation by a temporal inhibition of Kif2b activity.", "journal": "Scientific reports", "date": "2016", "authors": "Qin B, Cao D, Wu H, Mo F, Shao H, Chu J, Powell M, Aikhionbare F, Wang D, Fu C, He P, Pan W, Wang W, Liu X, Yao X", "evidence": [ { "database": "iPTMnet", "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448" } ], "reference": [ { "type": "PubMed", "id": "27982129", "url": "https://glygen.org/publication/PubMed/27982129" } ] } ], "crossref": [ { "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "27982129", "url": "https://glygen.org/publication/PubMed/27982129", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CLAILESKGLDPALGSETLA", "down_seq": "RQESTTDHMDSMLLLETLQE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448" }, { "database": "PubMed", "id": "27982129", "url": "https://glygen.org/publication/PubMed/27982129" } ], "site_lbl": "Ser237" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9Y448-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9Y448-1.232.232", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9Y448-1.248.248", "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": "Q9Y448-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "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": "Q9Y448-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448", "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": "PALGSETLASRQESTTDHMD", "down_seq": "MLLLETLQEELKLFNETAKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser248" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9Y448-1.232.232", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9Y448-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9Y448-1.264.264", "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": "Q9Y448-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "Q9Y448-1", "length": 316, "uniprot_id": "SKAP_HUMAN", "protein_name": "Small kinetochore-associated protein", "refseq_ac": "NP_001136233", "refseq_name": "small kinetochore-associated protein isoform b", "gene_name": "KNSTRN", "gene_names_uniprotkb": "KNSTRN; C15orf23; HSD11; SKAP; TRAF4AF1", "gene_names_refseq": "C15orf23; HSD11; KNSTRN; ROCHIS; SKAP; TRAF4AF1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9Y448", "url": "https://www.uniprot.org/uniprotkb/Q9Y448" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of SKAP by GSK3beta ensures chromosome segregation by a temporal inhibition of Kif2b activity.", "journal": "Scientific reports", "date": "2016", "authors": "Qin B, Cao D, Wu H, Mo F, Shao H, Chu J, Powell M, Aikhionbare F, Wang D, Fu C, He P, Pan W, Wang W, Liu X, Yao X", "evidence": [ { "database": "iPTMnet", "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448" } ], "reference": [ { "type": "PubMed", "id": "27982129", "url": "https://glygen.org/publication/PubMed/27982129" } ] }, { "title": "Phosphorylation of small kinetochore-associated protein induced by GSK3beta promotes cell migration and invasion in esophageal cancer.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2022", "authors": "Qin B, Zhu Z, Yin F, Yan D, Wan J, Dong M, Wang Z", "evidence": [ { "database": "RefSeq", "id": "NP_001136233", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001136233" }, { "database": "iPTMnet", "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448" } ], "reference": [ { "type": "PubMed", "id": "35201967", "url": "https://glygen.org/publication/PubMed/35201967" } ] } ], "crossref": [ { "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "27982129", "url": "https://glygen.org/publication/PubMed/27982129", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35201967", "url": "https://glygen.org/publication/PubMed/35201967", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QALKVKLEMKEERVRFLEQQ", "down_seq": "LCNNQVNDLTTALKEMEQLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9Y448", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9Y448" }, { "database": "PubMed", "id": "27982129", "url": "https://glygen.org/publication/PubMed/27982129" }, { "database": "PubMed", "id": "35201967", "url": "https://glygen.org/publication/PubMed/35201967" } ], "site_lbl": "Thr294" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "56", "end_pos": "56" } ] }, { "type": "snv", "site_list": [ { "start_pos": "24", "end_pos": "24" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "294", "end_pos": "294" } ] } ], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95232-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" }, { "database": "O-GlcNAc Atlas", "id": "O95232", "url": "https://oglcnac.org/atlas/detail/O95232" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] } ], "crossref": [ { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "https://oglcnac.org/atlas/detail/O95232", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O95232", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEEEREKERARDRERRKRSR", "down_seq": "RSRHSSRTSDRRCSRSRDHK", "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": "Ser295", "evidence": [ { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "O95232", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O95232" } ] } ], "snv": [ { "evidence": [ { "id": "O95232", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "606", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "17", "chr_pos": "50745910", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S295", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O95232-1.297.297", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "O95232-1.297.297", "start_pos": 297, "end_pos": 297, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" }, { "database": "O-GlcNAc Atlas", "id": "O95232", "url": "https://oglcnac.org/atlas/detail/O95232" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "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": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "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": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "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": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "https://oglcnac.org/atlas/detail/O95232", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O95232", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEREKERARDRERRKRSRSR", "down_seq": "RHSSRTSDRRCSRSRDHKRS", "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": "Ser297", "evidence": [ { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "O95232", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "O95232", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O95232" } ] } ], "snv": [ { "evidence": [ { "id": "O95232", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->C).", "chr_id": "17", "chr_pos": "50745915", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S297", "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": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O95232-1.295.295", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95232-1.410.410", "start_pos": 410, "end_pos": 410, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" }, { "database": "O-GlcNAc Atlas", "id": "O95232", "url": "https://oglcnac.org/atlas/detail/O95232" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] } ], "crossref": [ { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "https://oglcnac.org/atlas/detail/O95232", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SVKSGSREKQSEDTNTESKE", "down_seq": "DTKNEVNGTSEDIKSEGDTQ", "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": "Ser410", "evidence": [ { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "O95232", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O95232" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O95232-1.412.412", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O95232-1.419.419", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O95232-1.420.420", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O95232-1.425.425", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O95232-1.429.429", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95232-1.412.412", "start_pos": 412, "end_pos": 412, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" }, { "database": "O-GlcNAc Atlas", "id": "O95232", "url": "https://oglcnac.org/atlas/detail/O95232" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] } ], "crossref": [ { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "https://oglcnac.org/atlas/detail/O95232", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs768273933", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768273933", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768273933", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768273933", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768273933", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768273933", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KSGSREKQSEDTNTESKESD", "down_seq": "KNEVNGTSEDIKSEGDTQSN", "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": "Thr412", "evidence": [ { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "O95232", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O95232" } ] } ], "snv": [ { "evidence": [ { "id": "rs768273933", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768273933" }, { "id": "rs768273933", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768273933" }, { "id": "rs768273933", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768273933" } ], "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": "17", "chr_pos": "50750597", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T412", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O95232-1.410.410", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O95232-1.419.419", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O95232-1.420.420", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O95232-1.425.425", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O95232-1.429.429", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O95232-1.431.431", "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": 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": "O95232-1.419.419", "start_pos": 419, "end_pos": 419, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" }, { "database": "O-GlcNAc Atlas", "id": "O95232", "url": "https://oglcnac.org/atlas/detail/O95232" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "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": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "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": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "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": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "https://oglcnac.org/atlas/detail/O95232", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs149481569", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149481569", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs149481569", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149481569", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs149481569", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149481569", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs149481569", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149481569#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs149481569", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149481569", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QSEDTNTESKESDTKNEVNG", "down_seq": "SEDIKSEGDTQSN", "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": "Thr419", "evidence": [ { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "O95232", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95232" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "O95232", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O95232" } ] } ], "snv": [ { "evidence": [ { "id": "rs149481569", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149481569" }, { "id": "rs149481569", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149481569" }, { "id": "rs149481569", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149481569" }, { "id": "rs149481569", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149481569#frequency_tab" }, { "id": "rs149481569", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149481569" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "17", "chr_pos": "50750618", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "T419", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O95232-1.410.410", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O95232-1.412.412", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O95232-1.420.420", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O95232-1.425.425", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O95232-1.429.429", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O95232-1.431.431", "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": 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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95232-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95232", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "SQNQQSSGAAGPTGKNEEKI", "down_seq": "VLTDKIDVLLQQIEELGSEG", "snv": [ { "evidence": [ { "id": "O95232", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "50741693", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Q130", "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": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O95232-1.110.110", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "O95232-1.115.115", "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": "O95232-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs371275354", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371275354", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371275354", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371275354", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371275354", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371275354", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MISAAQLLDELMGRDRNL", "down_seq": "PDEKRSNVRWDHESVCKYYL", "snv": [ { "evidence": [ { "id": "rs371275354", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371275354" }, { "id": "rs371275354", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371275354" }, { "id": "rs371275354", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371275354" } ], "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": "17", "chr_pos": "50719787", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A19", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O95232-1.3.3", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O95232-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O95232-1.33.33", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95232-1.31.31", "start_pos": 31, "end_pos": 31, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95232", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs764272372", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764272372", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764272372", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764272372", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764272372", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764272372", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs764272372", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764272372", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LMGRDRNLAPDEKRSNVRWD", "down_seq": "ESVCKYYLCGFCPAELFTNT", "snv": [ { "evidence": [ { "id": "O95232", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232" }, { "id": "rs764272372", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764272372" }, { "id": "rs764272372", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764272372" }, { "id": "rs764272372", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764272372" }, { "id": "rs764272372", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764272372" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HES->NES).", "chr_id": "17", "chr_pos": "50719823", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H31", "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": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O95232-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O95232-1.33.33", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "O95232-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1441444618", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1441444618", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1441444618", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1441444618", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GRDRNLAPDEKRSNVRWDHE", "down_seq": "VCKYYLCGFCPAELFTNTRS", "snv": [ { "evidence": [ { "id": "rs1441444618", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1441444618" }, { "id": "rs1441444618", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1441444618" } ], "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 (SVC->NVC).", "chr_id": "17", "chr_pos": "50719830", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S33", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O95232-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O95232-1.31.31", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95232-1.365.365", "start_pos": 365, "end_pos": 365, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1249957255", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1249957255", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1249957255", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1249957255", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRSRDRRRSKSRDRKSYKHR", "down_seq": "KSRDREQDRKSKEKEKRGSD", "snv": [ { "evidence": [ { "id": "rs1249957255", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1249957255" }, { "id": "rs1249957255", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1249957255" } ], "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": "17", "chr_pos": "50746658", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S365", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "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": "O95232-1.387.387", "start_pos": 387, "end_pos": 387, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95232", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SRDREQDRKSKEKEKRGSDD", "down_seq": "KSSVKSGSREKQSEDTNTES", "snv": [ { "evidence": [ { "id": "O95232", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232" } ], "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": "17", "chr_pos": "50750523", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K387", "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": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "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": "O95232-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95232", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RSDLGPCEKIHDENLRKQYE", "down_seq": "SSRFMKVGYERDFLRYLQSL", "snv": [ { "evidence": [ { "id": "O95232", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95232" } ], "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 (KSS->NSS).", "chr_id": "17", "chr_pos": "50741111", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K72", "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": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "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": "O95232-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.", "journal": "Science (New York, N.Y.)", "date": "2007", "authors": "Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ", "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] }, { "title": "Profiling of UV-induced ATM/ATR signaling pathways.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Stokes MP, Rush J, Macneill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] } ], "crossref": [ { "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QSLLAEVERRIRRGHARLAL", "down_seq": "QNQQSSGAAGPTGKNEEKIQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ], "site_lbl": "Ser110" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "O95232-1.115.115", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O95232-1.130.130", "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": "O95232-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "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": "EVERRIRRGHARLALSQNQQ", "down_seq": "SGAAGPTGKNEEKIQVLTDK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser115" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "O95232-1.110.110", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O95232-1.130.130", "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": "O95232-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "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": "MGYAKIKATVEELKEKLRKR", "down_seq": "EEPDRDERLKKEKQEREERE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr238" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "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": "O95232-1.333.333", "start_pos": 333, "end_pos": 333, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "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": "DHKRSRSRERRRSRSRDRRR", "down_seq": "RSHDRSERKHRSRSRDRRRS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser333" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O95232-1.335.335", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O95232-1.339.339", "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": "O95232-1.335.335", "start_pos": 335, "end_pos": 335, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "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": "KRSRSRERRRSRSRDRRRSR", "down_seq": "HDRSERKHRSRSRDRRRSKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser335" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O95232-1.333.333", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O95232-1.339.339", "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": "O95232-1.339.339", "start_pos": 339, "end_pos": 339, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "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": "SRERRRSRSRDRRRSRSHDR", "down_seq": "ERKHRSRSRDRRRSKSRDRK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser339" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "O95232-1.333.333", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O95232-1.335.335", "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": "O95232-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MI", "down_seq": "AAQLLDELMGRDRNLAPDEK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" } ], "site_lbl": "Ser3" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "O95232-1.19.19", "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": "O95232-1.420.420", "start_pos": 420, "end_pos": 420, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SEDTNTESKESDTKNEVNGT", "down_seq": "EDIKSEGDTQSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser420" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O95232-1.410.410", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "O95232-1.412.412", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O95232-1.419.419", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O95232-1.425.425", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O95232-1.429.429", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O95232-1.431.431", "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": "O95232-1.425.425", "start_pos": 425, "end_pos": 425, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "title": "Profiling of UV-induced ATM/ATR signaling pathways.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Stokes MP, Rush J, Macneill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] }, { "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": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "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": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TESKESDTKNEVNGTSEDIK", "down_seq": "EGDTQSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "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": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser425" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O95232-1.410.410", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "O95232-1.412.412", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O95232-1.419.419", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O95232-1.420.420", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O95232-1.429.429", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O95232-1.431.431", "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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95232-1.429.429", "start_pos": 429, "end_pos": 429, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.", "journal": "Science (New York, N.Y.)", "date": "2007", "authors": "Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ", "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] }, { "title": "Profiling of UV-induced ATM/ATR signaling pathways.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Stokes MP, Rush J, Macneill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] }, { "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ESDTKNEVNGTSEDIKSEGD", "down_seq": "QSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr429" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O95232-1.410.410", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "O95232-1.412.412", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O95232-1.419.419", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O95232-1.420.420", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O95232-1.425.425", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O95232-1.431.431", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95232-1.431.431", "start_pos": 431, "end_pos": 431, "uniprot_canonical_ac": "O95232-1", "length": 432, "uniprot_id": "LC7L3_HUMAN", "protein_name": "Luc7-like protein 3", "refseq_ac": "NP_006098", "refseq_name": "luc7-like protein 3 isoform 1", "gene_name": "LUC7L3", "gene_names_uniprotkb": "LUC7L3; CREAP1; CROP; O48", "gene_names_refseq": "CRA; CREAP-1; CROP; LUC7A; LUC7L3; OA48-18; hLuc7A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" } ], "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Profiling of UV-induced ATM/ATR signaling pathways.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Stokes MP, Rush J, Macneill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] }, { "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": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Phosphoproteomic analysis of distinct tumor cell lines in response to nocodazole treatment.", "journal": "Proteomics", "date": "2009", "authors": "Nagano K, Shinkawa T, Mutoh H, Kondoh O, Morimoto S, Inomata N, Ashihara M, Ishii N, Aoki Y, Haramura M", "evidence": [ { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "O95232-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DTKNEVNGTSEDIKSEGDTQ", "down_seq": "", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95232", "url": "https://www.uniprot.org/uniprotkb/O95232" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95232", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95232" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Ser431" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "72", "end_pos": "72" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O95232-1.412.412", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "O95232-1.419.419", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "O95232-1.420.420", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O95232-1.425.425", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O95232-1.429.429", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs763250123", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763250123", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763250123", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763250123", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763250123", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763250123", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALTEKNKELEIAQDRNIAIQ", "down_seq": "QFTRTKEELEAEKRDLIRTN", "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": "Ser111", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs763250123", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763250123" }, { "id": "rs763250123", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763250123" }, { "id": "rs763250123", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763250123" } ], "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": "1", "chr_pos": "186367981", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S111", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1183.1183", "start_pos": 1183, "end_pos": 1183, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "rs1432670051", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1432670051", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1432670051", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1432670051#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1432670051", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1432670051", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1658597528", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658597528", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1658597528", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658597528#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IEKLSDKVVASVKEGVQGPL", "down_seq": "VSLSEEGKSQEQILEILRFI", "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": "VVASVKEGVQGPLNVSLSEEGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1183", "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" } ] } ], "snv": [ { "evidence": [ { "id": "rs1432670051", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1432670051" }, { "id": "rs1432670051", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1432670051#frequency_tab" }, { "id": "rs1432670051", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1432670051" } ], "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": "1", "chr_pos": "186343959", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1183", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1658597528", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658597528" }, { "id": "rs1658597528", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658597528#frequency_tab" } ], "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": "1", "chr_pos": "186343960", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1183", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P12270-1.1185.1185", "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": 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": 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": "P12270-1.1266.1266", "start_pos": 1266, "end_pos": 1266, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "REKVQVTAKTMAQHEELMKK", "down_seq": "ETMNVVMETNKMLREEKERL", "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": "Thr1266", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "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: o-glyco-site-loss (T->I).", "chr_id": "1", "chr_pos": "186341343", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T1266", "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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P12270-1.1252.1252", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.1255.1255", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P12270-1.1275.1275", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1275.1275", "start_pos": 1275, "end_pos": 1275, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TMAQHEELMKKTETMNVVME", "down_seq": "NKMLREEKERLEQDLQQMQA", "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": "Thr1275", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.1255.1255", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P12270-1.1266.1266", "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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1318.1318", "start_pos": 1318, "end_pos": 1318, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1658495816", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658495816", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1658495816", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658495816#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RKLELDILPLQEANAELSEK", "down_seq": "GMLQAEKKLLEEDVKRWKAR", "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": "Ser1318", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" }, { "id": "rs1658495816", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658495816" }, { "id": "rs1658495816", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658495816#frequency_tab" } ], "glycoeffect": [ "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: o-glyco-site-loss (S->G).", "chr_id": "1", "chr_pos": "186341096", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S1318", "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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1660.1660", "start_pos": 1660, "end_pos": 1660, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2102066775", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066775", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066775", "url": "https://www.ensembl.org/id/rs2102066775", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1658280141", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658280141", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1658280141", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658280141#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EQQRQITLKTTPASGERGIA", "down_seq": "TSDPPTANIKPTPVVSTPSK", "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": "Ser1660", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs2102066775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066775" }, { "id": "rs2102066775", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066775" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (STS->NTS); o-glyco-site-loss (S->N).", "chr_id": "1", "chr_pos": "186334528", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1660", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1658280141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658280141" }, { "id": "rs1658280141", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658280141#frequency_tab" } ], "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": "1", "chr_pos": "186334529", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1660", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1658280141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658280141" }, { "id": "rs1658280141", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658280141#frequency_tab" } ], "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": "1", "chr_pos": "186334529", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1660", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2102066775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066775" }, { "id": "rs2102066775", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066775" } ], "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": "1", "chr_pos": "186334528", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1660", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P12270-1.1658.1658", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.1661.1661", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.1662.1662", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.1666.1666", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P12270-1.1679.1679", "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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1661.1661", "start_pos": 1661, "end_pos": 1661, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs774674452", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774674452", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774674452", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774674452", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774674452", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774674452#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774674452", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774674452", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QQRQITLKTTPASGERGIAS", "down_seq": "SDPPTANIKPTPVVSTPSKV", "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": "Thr1661", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs774674452", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774674452" }, { "id": "rs774674452", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774674452" }, { "id": "rs774674452", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774674452#frequency_tab" }, { "id": "rs774674452", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774674452" } ], "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": "186334525", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1661", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774674452", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774674452" }, { "id": "rs774674452", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774674452" }, { "id": "rs774674452", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774674452#frequency_tab" }, { "id": "rs774674452", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774674452" } ], "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": "1", "chr_pos": "186334525", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1661", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P12270-1.1658.1658", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.1660.1660", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.1662.1662", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.1666.1666", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.1679.1679", "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": 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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1662.1662", "start_pos": 1662, "end_pos": 1662, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2102066764", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066764", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066764", "url": "https://www.ensembl.org/id/rs2102066764", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QRQITLKTTPASGERGIAST", "down_seq": "DPPTANIKPTPVVSTPSKVT", "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": "Ser1662", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs2102066764", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066764" }, { "id": "rs2102066764", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066764" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "1", "chr_pos": "186334522", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1662", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2102066764", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066764" }, { "id": "rs2102066764", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066764" } ], "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": "1", "chr_pos": "186334522", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1662", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P12270-1.1658.1658", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.1660.1660", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.1661.1661", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.1666.1666", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P12270-1.1679.1679", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.1682.1682", "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": 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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1666.1666", "start_pos": 1666, "end_pos": 1666, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1243993257", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1243993257", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1243993257", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1243993257", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs749391202", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749391202", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749391202", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749391202", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749391202", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749391202", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TLKTTPASGERGIASTSDPP", "down_seq": "ANIKPTPVVSTPSKVTAAAM", "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": "Thr1666", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs1243993257", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1243993257" }, { "id": "rs1243993257", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1243993257" } ], "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": "186334510", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1666", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1243993257", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1243993257" }, { "id": "rs1243993257", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1243993257" } ], "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": "1", "chr_pos": "186334510", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1666", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749391202", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749391202" }, { "id": "rs749391202", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749391202" }, { "id": "rs749391202", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749391202" } ], "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": "186334511", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1666", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1243993257", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1243993257" }, { "id": "rs1243993257", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1243993257" } ], "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": "1", "chr_pos": "186334510", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1666", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Thr1666" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P12270-1.1658.1658", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.1660.1660", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P12270-1.1661.1661", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.1662.1662", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.1679.1679", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.1682.1682", "categories": [ "glycosylation_flag", "snv_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": 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": 31 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1672.1672", "start_pos": 1672, "end_pos": 1672, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs2102066695", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066695", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066695", "url": "https://www.ensembl.org/id/rs2102066695", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ASGERGIASTSDPPTANIKP", "down_seq": "PVVSTPSKVTAAAMAGNKST", "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": "Thr1672", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] }, { "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": "Thr1672", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs2102066695", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066695" }, { "id": "rs2102066695", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066695" } ], "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": "186334492", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1672", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P12270-1.1658.1658", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P12270-1.1660.1660", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.1661.1661", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.1662.1662", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.1666.1666", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.1679.1679", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.1682.1682", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.1692.1692", "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": 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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1676.1676", "start_pos": 1676, "end_pos": 1676, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Cell-type-specific labeling and profiling of glycans in living mice.", "journal": "Nature chemical biology", "date": "2022-06", "authors": "Fan Xinqi, Song Qitao, Sun De-En, Hao Yi, Wang Jingyang, Wang Chunting, Chen Xing", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511" } ] }, { "title": "O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.", "journal": "Molecular cell", "date": "2023-08-17", "authors": "Xu Chenchen, Pan Xiaoqing, Wang Dong, Guan Yuanyuan, Yang Wenyu, Chen Xing, Liu Ying", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] }, { "title": "OGA mutant aberrantly hydrolyzes O-GlcNAc modification from PDLIM7 to modulate p53 and cytoskeleton in promoting cancer cell malignancy.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-06-11", "authors": "Hu Chia-Wei, Wang Ao, Fan Dacheng, Worth Matthew, Chen Zhengwei, Huang Junfeng, Xie Jinshan, Macdonald John, Li Lingjun, Jiang Jiaoyang", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs2102066663", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066663", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066663", "url": "https://www.ensembl.org/id/rs2102066663", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "RGIASTSDPPTANIKPTPVV", "down_seq": "TPSKVTAAAMAGNKSTPRAS", "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": "Ser1676", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "id": "35513511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35513511" }, { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" }, { "id": "38838015", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38838015" }, { "id": "2850", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ] }, { "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": "Ser1676", "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": "rs2102066663", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066663" }, { "id": "rs2102066663", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066663" } ], "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": "1", "chr_pos": "186334480", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1676", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2102066663", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066663" }, { "id": "rs2102066663", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066663" } ], "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": "1", "chr_pos": "186334480", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1676", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1676" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P12270-1.1658.1658", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P12270-1.1660.1660", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.1661.1661", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P12270-1.1662.1662", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.1666.1666", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.1679.1679", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.1682.1682", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.1692.1692", "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": 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": 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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": 35 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1677.1677", "start_pos": 1677, "end_pos": 1677, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1447077712", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1447077712", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1447077712", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1447077712", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2102066648", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066648", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066648", "url": "https://www.ensembl.org/id/rs2102066648", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GIASTSDPPTANIKPTPVVS", "down_seq": "PSKVTAAAMAGNKSTPRASI", "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": "Thr1677", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs1447077712", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1447077712" }, { "id": "rs1447077712", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1447077712" } ], "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": "1", "chr_pos": "186334478", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1677", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2102066648", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066648" }, { "id": "rs2102066648", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066648" } ], "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": "186334477", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1677", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1447077712", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1447077712" }, { "id": "rs1447077712", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1447077712" } ], "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": "186334478", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1677", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Thr1677" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P12270-1.1658.1658", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P12270-1.1660.1660", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P12270-1.1661.1661", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.1662.1662", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.1666.1666", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.1679.1679", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.1682.1682", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.1692.1692", "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": 32 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1679.1679", "start_pos": 1679, "end_pos": 1679, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1658278705", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658278705", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1658278705", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658278705#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2102066634", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066634", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066634", "url": "https://www.ensembl.org/id/rs2102066634", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASTSDPPTANIKPTPVVSTP", "down_seq": "KVTAAAMAGNKSTPRASIRP", "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": "Ser1679", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" }, { "id": "rs1658278705", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658278705" }, { "id": "rs1658278705", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658278705#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->C).", "chr_id": "1", "chr_pos": "186334472", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1679", "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": "rs1658278705", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658278705" }, { "id": "rs1658278705", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658278705#frequency_tab" } ], "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": "1", "chr_pos": "186334472", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1679", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2102066634", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066634" }, { "id": "rs2102066634", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066634" } ], "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": "1", "chr_pos": "186334471", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1679", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P12270-1.1660.1660", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P12270-1.1661.1661", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P12270-1.1662.1662", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.1666.1666", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.1682.1682", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.1692.1692", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P12270-1.1698.1698", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1682.1682", "start_pos": 1682, "end_pos": 1682, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2102066617", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066617", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066617", "url": "https://www.ensembl.org/id/rs2102066617", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SDPPTANIKPTPVVSTPSKV", "down_seq": "AAAMAGNKSTPRASIRPMVT", "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": "Thr1682", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs2102066617", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066617" }, { "id": "rs2102066617", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066617" } ], "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": "186334462", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1682", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2102066617", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066617" }, { "id": "rs2102066617", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066617" } ], "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": "1", "chr_pos": "186334462", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1682", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.1662.1662", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P12270-1.1666.1666", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.1679.1679", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.1692.1692", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.1698.1698", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.1702.1702", "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": 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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1691.1691", "start_pos": 1691, "end_pos": 1691, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2102066520", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066520", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066520", "url": "https://www.ensembl.org/id/rs2102066520", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1488226303", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1488226303", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1488226303", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1488226303", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "PTPVVSTPSKVTAAAMAGNK", "down_seq": "TPRASIRPMVTPATVTNPTT", "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": "Ser1691", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs2102066520", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066520" }, { "id": "rs2102066520", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066520" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "1", "chr_pos": "186334435", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1691", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1488226303", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1488226303" }, { "id": "rs1488226303", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1488226303" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->A).", "chr_id": "1", "chr_pos": "186334436", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1691", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1691" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P12270-1.1679.1679", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P12270-1.1682.1682", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.1692.1692", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.1698.1698", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.1702.1702", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.1707.1707", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.1709.1709", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P12270-1.1710.1710", "categories": [ "snv_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": 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": 32 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1702.1702", "start_pos": 1702, "end_pos": 1702, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "rs2102066403", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066403", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066403", "url": "https://www.ensembl.org/id/rs2102066403", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2102066413", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066413", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066413", "url": "https://www.ensembl.org/id/rs2102066413", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TAAAMAGNKSTPRASIRPMV", "down_seq": "PATVTNPTTTPTATVMPTTQ", "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": "Thr1702", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs2102066403", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066403" }, { "id": "rs2102066403", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066403" } ], "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": "186334402", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1702", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2102066413", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066413" }, { "id": "rs2102066413", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066413" } ], "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": "186334403", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1702", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2102066403", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066403" }, { "id": "rs2102066403", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066403" } ], "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": "1", "chr_pos": "186334402", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1702", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.1682.1682", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.1692.1692", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.1698.1698", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.1707.1707", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.1709.1709", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P12270-1.1710.1710", "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": 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": "P12270-1.1804.1804", "start_pos": 1804, "end_pos": 1804, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis.", "journal": "Analytical chemistry", "date": "2008", "authors": "Wang B, Malik R, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1571610678", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571610678", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1571610678", "url": "https://www.ensembl.org/id/rs1571610678", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PQIEPANQELSSNIVEVVQS", "down_seq": "PVERPSTSTAVFGTVSATPS", "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": "Ser1804", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" }, { "id": "rs1571610678", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571610678" }, { "id": "rs1571610678", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1571610678" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->L).", "chr_id": "1", "chr_pos": "186333166", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1804", "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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ], "site_lbl": "Ser1804" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P12270-1.1808.1808", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P12270-1.1812.1812", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.1822.1822", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.1824.1824", "categories": [ "snv_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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": 31 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1812.1812", "start_pos": 1812, "end_pos": 1812, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELSSNIVEVVQSSPVERPST", "down_seq": "TAVFGTVSATPSSSLPKRTR", "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": "Ser1812", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P12270-1.1804.1804", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.1808.1808", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.1822.1822", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.1824.1824", "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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1822.1822", "start_pos": 1822, "end_pos": 1822, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "rs761969630", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761969630", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761969630", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761969630", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761969630", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761969630#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs761969630", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761969630", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QSSPVERPSTSTAVFGTVSA", "down_seq": "PSSSLPKRTREEEEDSTIEA", "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": "Thr1822", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs761969630", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761969630" }, { "id": "rs761969630", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761969630" }, { "id": "rs761969630", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761969630#frequency_tab" }, { "id": "rs761969630", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761969630" } ], "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": "186332334", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1822", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" }, { "id": "rs761969630", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761969630" }, { "id": "rs761969630", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761969630" }, { "id": "rs761969630", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761969630#frequency_tab" }, { "id": "rs761969630", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761969630" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "1", "chr_pos": "186332334", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1822", "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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P12270-1.1804.1804", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P12270-1.1808.1808", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.1812.1812", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.1824.1824", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.1837.1837", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.1838.1838", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P12270-1.1839.1839", "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", "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": "P12270-1.2060.2060", "start_pos": 2060, "end_pos": 2060, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] } ], "crossref": [ { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GNTGAAESSFSQEVSREQQP", "down_seq": "SASERQAPRAPQSPRRPPHP", "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": "Ser2060", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "1", "chr_pos": "186323805", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S2060", "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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P12270-1.2043.2043", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.2047.2047", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P12270-1.2048.2048", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.2050.2050", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.2054.2054", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.2061.2061", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.2063.2063", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.2073.2073", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.2074.2074", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "P12270-1.2061.2061", "start_pos": 2061, "end_pos": 2061, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] } ], "crossref": [ { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTGAAESSFSQEVSREQQPS", "down_seq": "ASERQAPRAPQSPRRPPHPL", "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": "Ser2061", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P12270-1.2043.2043", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P12270-1.2047.2047", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.2048.2048", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.2050.2050", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P12270-1.2054.2054", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.2060.2060", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.2063.2063", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.2073.2073", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.2074.2074", "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": "P12270-1.2063.2063", "start_pos": 2063, "end_pos": 2063, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs201007532", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201007532", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201007532", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201007532", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201007532", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201007532", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201007532", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201007532#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201007532", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201007532", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAAESSFSQEVSREQQPSSA", "down_seq": "ERQAPRAPQSPRRPPHPLPP", "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": "Ser2063", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs201007532", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201007532" }, { "id": "rs201007532", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201007532" }, { "id": "rs201007532", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201007532" }, { "id": "rs201007532", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201007532#frequency_tab" }, { "id": "rs201007532", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201007532" } ], "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": "1", "chr_pos": "186323795", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "S2063", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.2043.2043", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P12270-1.2047.2047", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.2048.2048", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.2050.2050", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P12270-1.2054.2054", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.2060.2060", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.2061.2061", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.2073.2073", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.2074.2074", "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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2176.2176", "start_pos": 2176, "end_pos": 2176, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs746203522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746203522", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746203522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746203522", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746203522", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746203522#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs746203522", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746203522", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PQVAGVPRFRFGPPEDMPQT", "down_seq": "SSHSDLGQLASQGGLGMYET", "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": "Ser2176", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] }, { "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": "Ser2176", "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": "rs746203522", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746203522" }, { "id": "rs746203522", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746203522" }, { "id": "rs746203522", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746203522#frequency_tab" }, { "id": "rs746203522", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746203522" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (SSS->NSS); o-glyco-site-loss (S->N).", "chr_id": "1", "chr_pos": "186320353", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2176", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P12270-1.2175.2175", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.2178.2178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.2180.2180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.2187.2187", "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": 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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2180.2180", "start_pos": 2180, "end_pos": 2180, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "GVPRFRFGPPEDMPQTSSSH", "down_seq": "DLGQLASQGGLGMYETPLFL", "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": "Ser2180", "evidence": [ { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser2180" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P12270-1.2175.2175", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.2176.2176", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.2178.2178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.2187.2187", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "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": 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": "P12270-1.2187.2187", "start_pos": 2187, "end_pos": 2187, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GPPEDMPQTSSSHSDLGQLA", "down_seq": "QGGLGMYETPLFLAHEEESG", "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": "Ser2187", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P12270-1.2175.2175", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.2176.2176", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P12270-1.2178.2178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P12270-1.2180.2180", "categories": [ "glycosylation_flag", "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": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2330.2330", "start_pos": 2330, "end_pos": 2330, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Artificial Cysteine S-Glycosylation Induced by Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry.", "journal": "Proteomics", "date": "2015", "authors": "Zhao P, Schulz TC, Sherrer ES, Weatherly DB, Robins AJ, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2016", "authors": "Lund PJ, Elias JE, Davis MM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "27655845", "url": "https://glygen.org/publication/PubMed/27655845" } ] }, { "title": "Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.", "journal": "Journal of proteome research", "date": "2011", "authors": "Parker BL, Gupta P, Cordwell SJ, Larsen MR, Palmisano G", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome.", "journal": "The Analyst", "date": "2021", "authors": "Fan Z, Li J, Liu T, Zhang Z, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" }, { "database": "GlyConnect", "id": "2850", "url": "https://glyconnect.expasy.org/browser/proteins/2850" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "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": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "27114449", "url": "https://glygen.org/publication/PubMed/27114449", "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": "27655845", "url": "https://glygen.org/publication/PubMed/27655845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21158410", "url": "https://glygen.org/publication/PubMed/21158410", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1657538065", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1657538065", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1657538065", "url": "https://www.ensembl.org/id/rs1657538065", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SSSVDTSSSQPKPFRRVRLQ", "down_seq": "TLRQGVRGRQFNRQRGVSHA", "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": "Thr2330", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P12270", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "22661428", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22661428" }, { "id": "36240223", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36240223" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "27114449", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27114449" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "27655845", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/27655845" }, { "id": "21158410", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21158410" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "20068230", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20068230" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs1657538065", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1657538065" }, { "id": "rs1657538065", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1657538065" } ], "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": "1", "chr_pos": "186314677", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2330", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P12270-1.2316.2316", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.2331.2331", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 30 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2331.2331", "start_pos": 2331, "end_pos": 2331, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] } ], "crossref": [ { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs368457946", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368457946", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs368457946", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368457946", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs368457946", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368457946#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs368457946", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368457946", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SSVDTSSSQPKPFRRVRLQT", "down_seq": "LRQGVRGRQFNRQRGVSHAM", "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": "Thr2331", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs368457946", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368457946" }, { "id": "rs368457946", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368457946" }, { "id": "rs368457946", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368457946#frequency_tab" }, { "id": "rs368457946", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368457946" } ], "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": "1", "chr_pos": "186314674", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2331", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P12270-1.2316.2316", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.2330.2330", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P12270-1.650.650", "start_pos": 650, "end_pos": 650, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "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": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1659008972", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1659008972", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1659008972", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1659008972#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1659008972", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1659008972", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1245628727", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245628727", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1245628727", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1245628727#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ASSLDDVSLASTPKRPSTSQ", "down_seq": "VSTPAPVPVIESTEAIEAKA", "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": "Thr650", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" }, { "id": "rs1659008972", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1659008972" }, { "id": "rs1659008972", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1659008972#frequency_tab" }, { "id": "rs1659008972", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1659008972" } ], "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: o-glyco-site-loss (T->I).", "chr_id": "1", "chr_pos": "186355708", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T650", "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" ] }, { "evidence": [ { "id": "rs1245628727", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245628727" }, { "id": "rs1245628727", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1245628727#frequency_tab" } ], "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": "186355709", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T650", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr650" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P12270-1.632.632", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.635.635", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P12270-1.641.641", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.646.646", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.652.652", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.653.653", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.663.663", "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": 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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.652.652", "start_pos": 652, "end_pos": 652, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs747256939", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747256939", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747256939", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747256939", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747256939", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747256939", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "SLDDVSLASTPKRPSTSQTV", "down_seq": "TPAPVPVIESTEAIEAKAAL", "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": "Ser652", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs747256939", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747256939" }, { "id": "rs747256939", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747256939" }, { "id": "rs747256939", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747256939" } ], "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": "1", "chr_pos": "186355702", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S652", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser652" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.632.632", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P12270-1.635.635", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.641.641", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.646.646", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P12270-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.650.650", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.653.653", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.663.663", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P12270-1.804.804", "start_pos": 804, "end_pos": 804, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P12270", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P12270" }, { "database": "O-GlcNAc Atlas", "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] } ], "crossref": [ { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://oglcnac.org/atlas/detail/P12270", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs547487756", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547487756", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs547487756", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs547487756", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs547487756", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547487756", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs547487756", "url": "http://gnomad.broadinstitute.org/awesome?query=rs547487756", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKKEKEMLKLSEVRLSQQRE", "down_seq": "LLAEQRGQNLLLTNLQTIQG", "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": "Ser804", "evidence": [ { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "P12270", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P12270" } ] } ], "snv": [ { "evidence": [ { "id": "rs547487756", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547487756" }, { "id": "rs547487756", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs547487756" }, { "id": "rs547487756", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547487756" }, { "id": "rs547487756", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs547487756" } ], "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": "1", "chr_pos": "186352034", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S804", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs547487756", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547487756" }, { "id": "rs547487756", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs547487756" }, { "id": "rs547487756", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs547487756" }, { "id": "rs547487756", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs547487756" } ], "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": "1", "chr_pos": "186352034", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S804", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": 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": "P12270-1.458.458", "start_pos": 458, "end_pos": 458, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Amino acid substitutions of coiled-coil protein Tpr abrogate anchorage to the nuclear pore complex but not parallel, in-register homodimerization.", "journal": "Molecular biology of the cell", "date": "2001", "authors": "Hase ME, Kuznetsov NV, Cordes VC", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "Reactome", "id": "R-HSA-5619107", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5619107" } ], "reference": [ { "type": "PubMed", "id": "11514627", "url": "https://glygen.org/publication/PubMed/11514627" } ] }, { "title": "Direct interaction with nup153 mediates binding of Tpr to the periphery of the nuclear pore complex.", "journal": "Molecular biology of the cell", "date": "2003", "authors": "Hase ME, Cordes VC", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "Reactome", "id": "R-HSA-5619107", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5619107" } ], "reference": [ { "type": "PubMed", "id": "12802065", "url": "https://glygen.org/publication/PubMed/12802065" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11514627", "url": "https://glygen.org/publication/PubMed/11514627", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12802065", "url": "https://glygen.org/publication/PubMed/12802065", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "KRQREEYERAQKAVASLSVK", "down_seq": "EQAMKEIQRLQEDTDKANKQ", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "P", "comment": "Diminishes association to NPC but not homodimerization. Inhibits association to NPC, interaction with NUP153 and nuclear membrane localization but not homodimerization; when associated with P-489.", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "11514627", "url": "https://glygen.org/publication/PubMed/11514627" }, { "database": "PubMed", "id": "12802065", "url": "https://glygen.org/publication/PubMed/12802065" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P12270-1.453.453", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.489.489", "start_pos": 489, "end_pos": 489, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Amino acid substitutions of coiled-coil protein Tpr abrogate anchorage to the nuclear pore complex but not parallel, in-register homodimerization.", "journal": "Molecular biology of the cell", "date": "2001", "authors": "Hase ME, Kuznetsov NV, Cordes VC", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "Reactome", "id": "R-HSA-5619107", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5619107" } ], "reference": [ { "type": "PubMed", "id": "11514627", "url": "https://glygen.org/publication/PubMed/11514627" } ] }, { "title": "Direct interaction with nup153 mediates binding of Tpr to the periphery of the nuclear pore complex.", "journal": "Molecular biology of the cell", "date": "2003", "authors": "Hase ME, Cordes VC", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "Reactome", "id": "R-HSA-5619107", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5619107" } ], "reference": [ { "type": "PubMed", "id": "12802065", "url": "https://glygen.org/publication/PubMed/12802065" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11514627", "url": "https://glygen.org/publication/PubMed/11514627", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12802065", "url": "https://glygen.org/publication/PubMed/12802065", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "QEDTDKANKQSSVLERDNRR", "down_seq": "EIQVKDLSQQIRVLLMELEE", "mutagenesis": [ { "sequence_org": "M", "sequence_mut": "P", "comment": "Diminishes association to NPC but not homodimerization. Inhibits association to NPC, interaction with NUP153 and nuclear membrane localization but not homodimerization; when associated with P-458.", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "11514627", "url": "https://glygen.org/publication/PubMed/11514627" }, { "database": "PubMed", "id": "12802065", "url": "https://glygen.org/publication/PubMed/12802065" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.552.552", "start_pos": 552, "end_pos": 552, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs373572751", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373572751", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373572751", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373572751", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373572751", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373572751#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs373572751", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373572751", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs373572751", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373572751", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VISQHLVSYRNIEELQQQNQ", "down_seq": "LLVALRELGETREREEQETT", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" }, { "id": "rs373572751", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373572751" }, { "id": "rs373572751", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373572751" }, { "id": "rs373572751", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373572751#frequency_tab" }, { "id": "rs373572751", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373572751" }, { "id": "rs373572751", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373572751" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); n-glyco-sequon-gain (NQR->NQC).", "chr_id": "1", "chr_pos": "186357467", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R552", "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: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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.1007.1007", "start_pos": 1007, "end_pos": 1007, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RKNIEVRLKESAEFQTQLEK", "down_seq": "LMEVEKEKQELQDDKRRAIE", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "186346210", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K1007", "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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.1096.1096", "start_pos": 1096, "end_pos": 1096, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VEAQNKYERELMLHAADVEA", "down_seq": "QAAKEQVSKMASVRQHLEET", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "186344505", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L1096", "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: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: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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.1204.1204", "start_pos": 1204, "end_pos": 1204, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VSLSEEGKSQEQILEILRFI", "down_seq": "REKEIAETRFEVAQVESLRY", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "186343466", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1204", "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: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: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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P12270-1.1185.1185", "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": "P12270-1.1394.1394", "start_pos": 1394, "end_pos": 1394, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EIGRLKAEIARSNASLTNNQ", "down_seq": "LIQSLKEDLNKVRTEKETIQ", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NQN->NQS).", "chr_id": "1", "chr_pos": "186338214", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N1394", "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": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P12270-1.1385.1385", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.1390.1390", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.1398.1398", "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": "P12270-1.140.140", "start_pos": 140, "end_pos": 140, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LEAEKRDLIRTNERLSQELE", "down_seq": "LTEDVKRLNEKLKESNTTKG", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2617", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "Y", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (YLT->NLT).", "chr_id": "1", "chr_pos": "186367895", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Y140", "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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P12270-1.135.135", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.155.155", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "P12270-1.1470.1470", "start_pos": 1470, "end_pos": 1470, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs766655194", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766655194", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766655194", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766655194", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766655194", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766655194", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "AQQDKVMETSAQSSGDHQEQ", "down_seq": "VSVQEMQELKETLNQAETKS", "snv": [ { "evidence": [ { "id": "rs766655194", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766655194" }, { "id": "rs766655194", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766655194" }, { "id": "rs766655194", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766655194" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HVS->NVS).", "chr_id": "1", "chr_pos": "186337111", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1470", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P12270-1.1458.1458", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.1459.1459", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P12270-1.1462.1462", "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": "P12270-1.1534.1534", "start_pos": 1534, "end_pos": 1534, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs767885837", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767885837", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767885837", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767885837", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767885837", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767885837#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs767885837", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767885837", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LQEQTVQLQSELSRLRQDLQ", "down_seq": "RTTQEEQLRQQITEKEEKTR", "snv": [ { "evidence": [ { "id": "rs767885837", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767885837" }, { "id": "rs767885837", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767885837" }, { "id": "rs767885837", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767885837#frequency_tab" }, { "id": "rs767885837", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767885837" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DRT->NRT).", "chr_id": "1", "chr_pos": "186336601", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1534", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777337605", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777337605", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777337605", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777337605", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777337605", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777337605#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777337605", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777337605", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SQELEYLTEDVKRLNEKLKE", "down_seq": "NTTKGELQLKLDELQASDVS", "snv": [ { "evidence": [ { "id": "rs777337605", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777337605" }, { "id": "rs777337605", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777337605" }, { "id": "rs777337605", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777337605#frequency_tab" }, { "id": "rs777337605", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777337605" } ], "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 (SNT->NNT).", "chr_id": "1", "chr_pos": "186363409", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S155", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.135.135", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.140.140", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P12270-1.1587.1587", "start_pos": 1587, "end_pos": 1587, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1456685932", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456685932", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1456685932", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456685932#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LAGVKDQLTKENEELKQRNG", "down_seq": "LDQQKDELDVRITALKSQYE", "snv": [ { "evidence": [ { "id": "rs1456685932", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456685932" }, { "id": "rs1456685932", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456685932#frequency_tab" } ], "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": "1", "chr_pos": "186335490", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1587", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.1658.1658", "start_pos": 1658, "end_pos": 1658, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1658298754", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658298754", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1658298754", "url": "https://www.ensembl.org/id/rs1658298754", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "VPEQQRQITLKTTPASGERG", "down_seq": "ASTSDPPTANIKPTPVVSTP", "snv": [ { "evidence": [ { "id": "rs1658298754", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658298754" }, { "id": "rs1658298754", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1658298754" } ], "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": "1", "chr_pos": "186335068", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1658", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P12270-1.1660.1660", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.1661.1661", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.1662.1662", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P12270-1.1666.1666", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P12270-1.1690.1690", "start_pos": 1690, "end_pos": 1690, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2102066525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066525", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066525", "url": "https://www.ensembl.org/id/rs2102066525", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KPTPVVSTPSKVTAAAMAGN", "down_seq": "STPRASIRPMVTPATVTNPT", "snv": [ { "evidence": [ { "id": "rs2102066525", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066525" }, { "id": "rs2102066525", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066525" } ], "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": "1", "chr_pos": "186334437", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1690", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.1679.1679", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P12270-1.1682.1682", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.1692.1692", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P12270-1.1698.1698", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.1702.1702", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P12270-1.1707.1707", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P12270-1.1709.1709", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.1710.1710", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P12270-1.1698.1698", "start_pos": 1698, "end_pos": 1698, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PSKVTAAAMAGNKSTPRASI", "down_seq": "PMVTPATVTNPTTTPTATVM", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "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 (5).", "chr_id": "1", "chr_pos": "186334415", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1698", "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: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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P12270-1.1679.1679", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P12270-1.1682.1682", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.1692.1692", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.1702.1702", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P12270-1.1707.1707", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.1709.1709", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.1710.1710", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "P12270-1.1707.1707", "start_pos": 1707, "end_pos": 1707, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AGNKSTPRASIRPMVTPATV", "down_seq": "NPTTTPTATVMPTTQVESQE", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "186334388", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T1707", "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: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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.1692.1692", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P12270-1.1698.1698", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P12270-1.1702.1702", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.1709.1709", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.1710.1710", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.1725.1725", "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": "P12270-1.1709.1709", "start_pos": 1709, "end_pos": 1709, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2102066336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066336", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102066336", "url": "https://www.ensembl.org/id/rs2102066336", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1658276783", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658276783", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1658276783", "url": "https://www.ensembl.org/id/rs1658276783", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NKSTPRASIRPMVTPATVTN", "down_seq": "TTTPTATVMPTTQVESQEAM", "snv": [ { "evidence": [ { "id": "rs2102066336", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102066336" }, { "id": "rs2102066336", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102066336" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPT->NAT).", "chr_id": "1", "chr_pos": "186334382", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1709", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1658276783", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658276783" }, { "id": "rs1658276783", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1658276783" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPT->NHT).", "chr_id": "1", "chr_pos": "186334381", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1709", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1658276783", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658276783" }, { "id": "rs1658276783", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1658276783" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPT->NLT).", "chr_id": "1", "chr_pos": "186334381", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1709", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" }, { "id": "rs1658276783", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658276783" }, { "id": "rs1658276783", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1658276783" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPT->NRT).", "chr_id": "1", "chr_pos": "186334381", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "P1709", "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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P12270-1.1692.1692", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.1698.1698", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P12270-1.1702.1702", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.1707.1707", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.1710.1710", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.1725.1725", "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": 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": 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": 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": "P12270-1.1710.1710", "start_pos": 1710, "end_pos": 1710, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KSTPRASIRPMVTPATVTNP", "down_seq": "TTPTATVMPTTQVESQEAMQ", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" }, { "id": "", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TTT->NTT).", "chr_id": "1", "chr_pos": "186334378", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1710", "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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P12270-1.1692.1692", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P12270-1.1698.1698", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P12270-1.1702.1702", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.1707.1707", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.1709.1709", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.1725.1725", "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": "P12270-1.1743.1743", "start_pos": 1743, "end_pos": 1743, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753401568", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753401568", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753401568", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753401568", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753401568", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753401568#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753401568", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753401568", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VESQEAMQSEGPVEHVPVFG", "down_seq": "TSGSVRSTSPNVQPSISQPI", "snv": [ { "evidence": [ { "id": "rs753401568", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753401568" }, { "id": "rs753401568", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753401568" }, { "id": "rs753401568", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753401568#frequency_tab" }, { "id": "rs753401568", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753401568" } ], "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": "1", "chr_pos": "186333349", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1743", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P12270-1.1725.1725", "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": "P12270-1.1808.1808", "start_pos": 1808, "end_pos": 1808, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PANQELSSNIVEVVQSSPVE", "down_seq": "PSTSTAVFGTVSATPSSSLP", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "186333155", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1808", "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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P12270-1.1804.1804", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.1812.1812", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.1822.1822", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.1824.1824", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "P12270-1.1824.1824", "start_pos": 1824, "end_pos": 1824, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1658190375", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658190375", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1658190375", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658190375#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPVERPSTSTAVFGTVSATP", "down_seq": "SSLPKRTREEEEDSTIEASD", "snv": [ { "evidence": [ { "id": "rs1658190375", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658190375" }, { "id": "rs1658190375", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658190375#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 (SSS->NSS).", "chr_id": "1", "chr_pos": "186332328", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1824", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.1804.1804", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P12270-1.1808.1808", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P12270-1.1812.1812", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.1822.1822", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.1837.1837", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.1838.1838", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.1839.1839", "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": "P12270-1.1837.1837", "start_pos": 1837, "end_pos": 1837, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770488579", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770488579", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770488579", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770488579", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770488579", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770488579", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GTVSATPSSSLPKRTREEEE", "down_seq": "STIEASDQVSDDTVEMPLPK", "snv": [ { "evidence": [ { "id": "rs770488579", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770488579" }, { "id": "rs770488579", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770488579" }, { "id": "rs770488579", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770488579" } ], "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": "186332290", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1837", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P12270-1.1822.1822", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.1824.1824", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.1838.1838", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.1839.1839", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.1847.1847", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.1850.1850", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P12270-1.1850.1850", "start_pos": 1850, "end_pos": 1850, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RTREEEEDSTIEASDQVSDD", "down_seq": "VEMPLPKKLKSVTPVGTEEE", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "T", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "1", "chr_pos": "186332250", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1850", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P12270-1.1837.1837", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P12270-1.1838.1838", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.1839.1839", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.1847.1847", "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": 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": "P12270-1.1985.1985", "start_pos": 1985, "end_pos": 1985, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YEEDEEDDDDDEDDTGMGDE", "down_seq": "EDSNEGTGSADGNDGYEADD", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "186326172", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G1985", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "P12270-1.2000.2000", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "P12270-1.2000.2000", "start_pos": 2000, "end_pos": 2000, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2102056684", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102056684", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102056684", "url": "https://www.ensembl.org/id/rs2102056684", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GMGDEGEDSNEGTGSADGND", "down_seq": "YEADDAEGGDGTDPGTETEE", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NDG->NDC).", "chr_id": "1", "chr_pos": "186326127", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G2000", "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": "rs2102056684", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102056684" }, { "id": "rs2102056684", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102056684" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDG->NDS).", "chr_id": "1", "chr_pos": "186326127", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G2000", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P12270-1.1985.1985", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P12270-1.2043.2043", "start_pos": 2043, "end_pos": 2043, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1370983792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1370983792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1370983792", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1370983792#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GGGEGNHRAADSQNSGEGNT", "down_seq": "AAESSFSQEVSREQQPSSAS", "snv": [ { "evidence": [ { "id": "rs1370983792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1370983792" }, { "id": "rs1370983792", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1370983792#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTG->NTS).", "chr_id": "1", "chr_pos": "186323856", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G2043", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P12270-1.2034.2034", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.2037.2037", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.2047.2047", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.2048.2048", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.2050.2050", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.2054.2054", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P12270-1.2060.2060", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.2061.2061", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.2063.2063", "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": "P12270-1.2073.2073", "start_pos": 2073, "end_pos": 2073, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "VSREQQPSSASERQAPRAPQ", "down_seq": "PRRPPHPLPPRLTIHAPPQE", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "186323765", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S2073", "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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser2073" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P12270-1.2054.2054", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.2060.2060", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P12270-1.2061.2061", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.2063.2063", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.2074.2074", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2074.2074", "start_pos": 2074, "end_pos": 2074, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SREQQPSSASERQAPRAPQS", "down_seq": "RRPPHPLPPRLTIHAPPQEL", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "186323762", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P2074", "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: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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.2054.2054", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P12270-1.2060.2060", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.2061.2061", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.2063.2063", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.2073.2073", "categories": [ "snv_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": "P12270-1.2145.2145", "start_pos": 2145, "end_pos": 2145, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HFFDDEDRTVPSTPTLVVPH", "down_seq": "TDGFAEAIHSPQVAGVPRFR", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "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 (3).", "chr_id": "1", "chr_pos": "186322346", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R2145", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P12270-1.2137.2137", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.2155.2155", "categories": [ "snv_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": "P12270-1.2155.2155", "start_pos": 2155, "end_pos": 2155, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of novel ERK2 substrates through use of an engineered kinase and ATP analogs.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Eblen ST, Kumar NV, Shah K, Henderson MJ, Watts CK, Shokat KM, Weber MJ", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "12594221", "url": "https://glygen.org/publication/PubMed/12594221" } ] }, { "title": "Large-scale discovery of ERK2 substrates identifies ERK-mediated transcriptional regulation by ETV3.", "journal": "Science signaling", "date": "2011", "authors": "Carlson SM, Chouinard CR, Labadorf A, Lam CJ, Schmelzle K, Fraenkel E, White FM", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "22028470", "url": "https://glygen.org/publication/PubMed/22028470" } ] }, { "title": "Extracellular signal-regulated kinase 2 (ERK2) phosphorylation sites and docking domain on the nuclear pore complex protein Tpr cooperatively regulate ERK2-Tpr interaction.", "journal": "Molecular and cellular biology", "date": "2008", "authors": "Vomastek T, Iwanicki MP, Burack WR, Tiwari D, Kumar D, Parsons JT, Weber MJ, Nandicoori VK", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis.", "journal": "Journal of proteome research", "date": "2008", "authors": "Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra.", "journal": "Journal of proteome research", "date": "2007", "authors": "Yu LR, Zhu Z, Chan KC, Issaq HJ, Dimitrov DS, Veenstra TD", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17924679", "url": "https://glygen.org/publication/PubMed/17924679" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008", "authors": "McNulty DE, Annan RS", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Immobilized metal affinity chromatography revisited: pH/acid control toward high selectivity in phosphoproteomics.", "journal": "Journal of proteome research", "date": "2008", "authors": "Tsai CF, Wang YT, Chen YR, Lai CY, Lin PY, Pan KT, Chen JY, Khoo KH, Chen YJ", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "title": "Phosphoproteomic analysis of distinct tumor cell lines in response to nocodazole treatment.", "journal": "Proteomics", "date": "2009", "authors": "Nagano K, Shinkawa T, Mutoh H, Kondoh O, Morimoto S, Inomata N, Ashihara M, Ishii N, Aoki Y, Haramura M", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ] }, { "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12594221", "url": "https://glygen.org/publication/PubMed/12594221", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22028470", "url": "https://glygen.org/publication/PubMed/22028470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17924679", "url": "https://glygen.org/publication/PubMed/17924679", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSTPTLVVPHRTDGFAEAIH", "down_seq": "PQVAGVPRFRFGPPEDMPQT", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "186320416", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S2155", "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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P28482-1", "kinase_gene_name": "MAPK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "12594221", "url": "https://glygen.org/publication/PubMed/12594221" }, { "database": "PubMed", "id": "22028470", "url": "https://glygen.org/publication/PubMed/22028470" }, { "database": "PubMed", "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356" } ], "site_lbl": "Ser2155" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "17924679", "url": "https://glygen.org/publication/PubMed/17924679" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser2155" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P12270-1.2137.2137", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.2145.2145", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.2175.2175", "categories": [ "phosphorylation_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": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "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": 18 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2178.2178", "start_pos": 2178, "end_pos": 2178, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "rs1223743120", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1223743120", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1223743120", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1223743120", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "VAGVPRFRFGPPEDMPQTSS", "down_seq": "HSDLGQLASQGGLGMYETPL", "snv": [ { "evidence": [ { "id": "rs1223743120", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1223743120" }, { "id": "rs1223743120", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1223743120" } ], "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": "1", "chr_pos": "186320347", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2178", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser2178" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P12270-1.2175.2175", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.2176.2176", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.2180.2180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P12270-1.2187.2187", "categories": [ "glycosylation_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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P12270-1.219.219", "start_pos": 219, "end_pos": 219, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2101986069", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101986069", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2101986069", "url": "https://www.ensembl.org/id/rs2101986069", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "TELKTKTDELLALGREKGNE", "down_seq": "LELKCNLENKKEEVSRLEEQ", "snv": [ { "evidence": [ { "id": "rs2101986069", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2101986069" }, { "id": "rs2101986069", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2101986069" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEI->NET).", "chr_id": "1", "chr_pos": "186362877", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I219", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.2228.2228", "start_pos": 2228, "end_pos": 2228, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1202472769", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1202472769", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1202472769", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1202472769", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GRSVPTTPLQVAAPVTVFTE", "down_seq": "TTSDASEHASQSVPMVTTST", "snv": [ { "evidence": [ { "id": "rs1202472769", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1202472769" }, { "id": "rs1202472769", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1202472769" } ], "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 (STT->NTT).", "chr_id": "1", "chr_pos": "186318585", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2228", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P12270-1.2214.2214", "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": "P12270-1.2316.2316", "start_pos": 2316, "end_pos": 2316, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758939822", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758939822", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758939822", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758939822", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758939822", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758939822#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs758939822", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758939822", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DESDLPSTSQDPPSSSSVDT", "down_seq": "SSQPKPFRRVRLQTTLRQGV", "snv": [ { "evidence": [ { "id": "rs758939822", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758939822" }, { "id": "rs758939822", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758939822" }, { "id": "rs758939822", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758939822#frequency_tab" }, { "id": "rs758939822", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758939822" } ], "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": "1", "chr_pos": "186314718", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2316", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "P12270-1.2330.2330", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.2331.2331", "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": "P12270-1.2363.2363", "start_pos": 2363, "end_pos": 2363, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1657474843", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1657474843", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1657474843", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1657474843#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1657474843", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1657474843", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RQRGVSHAMGGRGGINRGNI", "down_seq": "", "snv": [ { "evidence": [ { "id": "rs1657474843", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1657474843" }, { "id": "rs1657474843", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1657474843#frequency_tab" }, { "id": "rs1657474843", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1657474843" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIN->NIS).", "chr_id": "1", "chr_pos": "186313975", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2363", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.323.323", "start_pos": 323, "end_pos": 323, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1659166733", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1659166733", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1659166733", "url": "https://www.ensembl.org/id/rs1659166733", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LTRAVEELHKLLKEAGEANK", "down_seq": "IQDHLLEVEQSKDQMEKEML", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "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 (NKA->NKS).", "chr_id": "1", "chr_pos": "186360897", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A323", "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": "rs1659166733", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1659166733" }, { "id": "rs1659166733", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1659166733" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKA->NKT).", "chr_id": "1", "chr_pos": "186360897", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A323", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": 1 } ], "sort_fields": [ "subjects_tested", "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": "P12270-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1277851474", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1277851474", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1277851474", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1277851474", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QMEKEMLEKIGRLEKELENA", "down_seq": "DLLSATKRKGAILSEEELAA", "snv": [ { "evidence": [ { "id": "rs1277851474", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1277851474" }, { "id": "rs1277851474", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1277851474" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAN->NAS).", "chr_id": "1", "chr_pos": "186360794", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N357", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.453.453", "start_pos": 453, "end_pos": 453, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1391644698", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1391644698", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1391644698", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1391644698", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KAPILKRQREEYERAQKAVA", "down_seq": "LSVKLEQAMKEIQRLQEDTD", "snv": [ { "evidence": [ { "id": "rs1391644698", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1391644698" }, { "id": "rs1391644698", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1391644698" } ], "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": "1", "chr_pos": "186359830", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S453", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P12270-1.458.458", "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": "P12270-1.525.525", "start_pos": 525, "end_pos": 525, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MELEEARGNHVIRDEEVSSA", "down_seq": "ISSSSEVISQHLVSYRNIEE", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DIS->NIS).", "chr_id": "1", "chr_pos": "186357548", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D525", "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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P12270-1.522.522", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.527.527", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.529.529", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.530.530", "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": "P12270-1.609.609", "start_pos": 609, "end_pos": 609, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P12270", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELEQLRKSRQHQMQLVDSIV", "down_seq": "QRDMYRILLSQTTGVAIPLH", "snv": [ { "evidence": [ { "id": "P12270", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P12270" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "186356349", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R609", "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: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": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.635.635", "start_pos": 635, "end_pos": 635, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1659010551", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1659010551", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1659010551", "url": "https://www.ensembl.org/id/rs1659010551", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RILLSQTTGVAIPLHASSLD", "down_seq": "VSLASTPKRPSTSQTVSTPA", "snv": [ { "evidence": [ { "id": "rs1659010551", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1659010551" }, { "id": "rs1659010551", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1659010551" } ], "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": "1", "chr_pos": "186355754", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D635", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P12270-1.632.632", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.641.641", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.646.646", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.650.650", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P12270-1.652.652", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.653.653", "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": "P12270-1.958.958", "start_pos": 958, "end_pos": 958, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1658713680", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658713680", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1658713680", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658713680#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1658713680", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1658713680", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSQLRQTEEQVNDLKERLKT", "down_seq": "TSNVEQYQAMVTSLEESLNK", "snv": [ { "evidence": [ { "id": "rs1658713680", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1658713680" }, { "id": "rs1658713680", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1658713680#frequency_tab" }, { "id": "rs1658713680", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1658713680" } ], "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": "1", "chr_pos": "186347362", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S958", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.1185.1185", "start_pos": 1185, "end_pos": 1185, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] }, { "title": "Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages.", "journal": "Journal of proteome research", "date": "2009", "authors": "Malik R, Lenobel R, Santamaria A, Ries A, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" } ] }, { "title": "Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer.", "journal": "Analytical chemistry", "date": "2010", "authors": "Raijmakers R, Kraiczek K, de Jong AP, Mohammed S, Heck AJ", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KLSDKVVASVKEGVQGPLNV", "down_seq": "LSEEGKSQEQILEILRFIRR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" }, { "database": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ], "site_lbl": "Ser1185" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P12270-1.1183.1183", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P12270-1.1204.1204", "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": 16 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.1252.1252", "start_pos": 1252, "end_pos": 1252, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "ERELQELQDSLNAEREKVQV", "down_seq": "AKTMAQHEELMKKTETMNVV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr1252" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P12270-1.1255.1255", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.1266.1266", "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": "P12270-1.1255.1255", "start_pos": 1255, "end_pos": 1255, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "LQELQDSLNAEREKVQVTAK", "down_seq": "MAQHEELMKKTETMNVVMET", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr1255" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P12270-1.1252.1252", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.1266.1266", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.1275.1275", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "RTKEELEAEKRDLIRTNERL", "down_seq": "QELEYLTEDVKRLNEKLKES", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser135" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P12270-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.155.155", "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": "P12270-1.1385.1385", "start_pos": 1385, "end_pos": 1385, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "TKRIQQLTEEIGRLKAEIAR", "down_seq": "NASLTNNQNLIQSLKEDLNK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1385" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P12270-1.1390.1390", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P12270-1.1394.1394", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.1398.1398", "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": "P12270-1.1390.1390", "start_pos": 1390, "end_pos": 1390, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "QLTEEIGRLKAEIARSNASL", "down_seq": "NNQNLIQSLKEDLNKVRTEK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr1390" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P12270-1.1385.1385", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.1394.1394", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P12270-1.1398.1398", "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": "P12270-1.1398.1398", "start_pos": 1398, "end_pos": 1398, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "LKAEIARSNASLTNNQNLIQ", "down_seq": "LKEDLNKVRTEKETIQKDLD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1398" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P12270-1.1385.1385", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P12270-1.1390.1390", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.1394.1394", "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": "P12270-1.1458.1458", "start_pos": 1458, "end_pos": 1458, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "GRRYKTQYEELKAQQDKVME", "down_seq": "SAQSSGDHQEQHVSVQEMQE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr1458" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P12270-1.1459.1459", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.1462.1462", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.1470.1470", "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": "P12270-1.1459.1459", "start_pos": 1459, "end_pos": 1459, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "RRYKTQYEELKAQQDKVMET", "down_seq": "AQSSGDHQEQHVSVQEMQEL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1459" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P12270-1.1458.1458", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.1462.1462", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.1470.1470", "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": "P12270-1.1462.1462", "start_pos": 1462, "end_pos": 1462, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "KTQYEELKAQQDKVMETSAQ", "down_seq": "SGDHQEQHVSVQEMQELKET", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1462" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P12270-1.1458.1458", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.1459.1459", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P12270-1.1470.1470", "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": "P12270-1.1692.1692", "start_pos": 1692, "end_pos": 1692, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TPVVSTPSKVTAAAMAGNKS", "down_seq": "PRASIRPMVTPATVTNPTTT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "site_lbl": "Thr1692" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.1672.1672", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P12270-1.1676.1676", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.1677.1677", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.1679.1679", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.1682.1682", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.1690.1690", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.1691.1691", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.1698.1698", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.1702.1702", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.1707.1707", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P12270-1.1709.1709", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.1710.1710", "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": "P12270-1.1725.1725", "start_pos": 1725, "end_pos": 1725, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis.", "journal": "Analytical chemistry", "date": "2008", "authors": "Wang B, Malik R, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TVTNPTTTPTATVMPTTQVE", "down_seq": "QEAMQSEGPVEHVPVFGSTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ], "site_lbl": "Ser1725" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P12270-1.1707.1707", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P12270-1.1709.1709", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.1710.1710", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.1743.1743", "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": "P12270-1.1838.1838", "start_pos": 1838, "end_pos": 1838, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "TVSATPSSSLPKRTREEEED", "down_seq": "TIEASDQVSDDTVEMPLPKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1838" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P12270-1.1822.1822", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P12270-1.1824.1824", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.1837.1837", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.1839.1839", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P12270-1.1847.1847", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.1850.1850", "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": "P12270-1.1839.1839", "start_pos": 1839, "end_pos": 1839, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VSATPSSSLPKRTREEEEDS", "down_seq": "IEASDQVSDDTVEMPLPKKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr1839" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P12270-1.1822.1822", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.1824.1824", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.1837.1837", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.1838.1838", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P12270-1.1847.1847", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.1850.1850", "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": "P12270-1.1847.1847", "start_pos": 1847, "end_pos": 1847, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "LPKRTREEEEDSTIEASDQV", "down_seq": "DDTVEMPLPKKLKSVTPVGT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser1847" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P12270-1.1837.1837", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P12270-1.1838.1838", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P12270-1.1839.1839", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.1850.1850", "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": "P12270-1.1893.1893", "start_pos": 1893, "end_pos": 1893, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AEESTDGEVETQVYNQDSQD", "down_seq": "IGEGVTQGDYTPMEDSEETS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "site_lbl": "Ser1893" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.2034.2034", "start_pos": 2034, "end_pos": 2034, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.", "journal": "Science (New York, N.Y.)", "date": "2007", "authors": "Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] }, { "title": "Profiling of UV-induced ATM/ATR signaling pathways.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Stokes MP, Rush J, Macneill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PGTETEESMGGGEGNHRAAD", "down_seq": "QNSGEGNTGAAESSFSQEVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ], "site_lbl": "Ser2034" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P12270-1.2037.2037", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P12270-1.2043.2043", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.2047.2047", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.2048.2048", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.2050.2050", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.2054.2054", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2037.2037", "start_pos": 2037, "end_pos": 2037, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ETEESMGGGEGNHRAADSQN", "down_seq": "GEGNTGAAESSFSQEVSREQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser2037" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P12270-1.2034.2034", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.2043.2043", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.2047.2047", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.2048.2048", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.2050.2050", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P12270-1.2054.2054", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2047.2047", "start_pos": 2047, "end_pos": 2047, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Profiling of UV-induced ATM/ATR signaling pathways.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Stokes MP, Rush J, Macneill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GNHRAADSQNSGEGNTGAAE", "down_seq": "SFSQEVSREQQPSSASERQA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ], "site_lbl": "Ser2047" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P12270-1.2034.2034", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.2037.2037", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.2043.2043", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.2048.2048", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.2050.2050", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.2054.2054", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.2060.2060", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.2061.2061", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.2063.2063", "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": "P12270-1.2048.2048", "start_pos": 2048, "end_pos": 2048, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages.", "journal": "Journal of proteome research", "date": "2009", "authors": "Malik R, Lenobel R, Santamaria A, Ries A, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289", "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": "NHRAADSQNSGEGNTGAAES", "down_seq": "FSQEVSREQQPSSASERQAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser2048" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P12270-1.2034.2034", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.2037.2037", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P12270-1.2043.2043", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.2047.2047", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.2050.2050", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.2054.2054", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.2060.2060", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.2061.2061", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.2063.2063", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2050.2050", "start_pos": 2050, "end_pos": 2050, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.", "journal": "Science (New York, N.Y.)", "date": "2007", "authors": "Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "title": "Profiling of UV-induced ATM/ATR signaling pathways.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Stokes MP, Rush J, Macneill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] }, { "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages.", "journal": "Journal of proteome research", "date": "2009", "authors": "Malik R, Lenobel R, Santamaria A, Ries A, Nigg EA, Korner R", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RAADSQNSGEGNTGAAESSF", "down_seq": "QEVSREQQPSSASERQAPRA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" } ], "site_lbl": "Ser2050" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P12270-1.2034.2034", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.2037.2037", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P12270-1.2043.2043", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.2047.2047", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.2048.2048", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.2054.2054", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.2060.2060", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.2061.2061", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P12270-1.2063.2063", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2054.2054", "start_pos": 2054, "end_pos": 2054, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "SQNSGEGNTGAAESSFSQEV", "down_seq": "REQQPSSASERQAPRAPQSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser2054" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.2034.2034", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P12270-1.2037.2037", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.2043.2043", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P12270-1.2047.2047", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.2048.2048", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.2050.2050", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.2060.2060", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.2061.2061", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P12270-1.2063.2063", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P12270-1.2073.2073", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.2074.2074", "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": "P12270-1.2116.2116", "start_pos": 2116, "end_pos": 2116, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of novel ERK2 substrates through use of an engineered kinase and ATP analogs.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Eblen ST, Kumar NV, Shah K, Henderson MJ, Watts CK, Shokat KM, Weber MJ", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "12594221", "url": "https://glygen.org/publication/PubMed/12594221" } ] }, { "title": "Large-scale discovery of ERK2 substrates identifies ERK-mediated transcriptional regulation by ETV3.", "journal": "Science signaling", "date": "2011", "authors": "Carlson SM, Chouinard CR, Labadorf A, Lam CJ, Schmelzle K, Fraenkel E, White FM", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "22028470", "url": "https://glygen.org/publication/PubMed/22028470" } ] }, { "title": "Extracellular signal-regulated kinase 2 (ERK2) phosphorylation sites and docking domain on the nuclear pore complex protein Tpr cooperatively regulate ERK2-Tpr interaction.", "journal": "Molecular and cellular biology", "date": "2008", "authors": "Vomastek T, Iwanicki MP, Burack WR, Tiwari D, Kumar D, Parsons JT, Weber MJ, Nandicoori VK", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12594221", "url": "https://glygen.org/publication/PubMed/12594221", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22028470", "url": "https://glygen.org/publication/PubMed/22028470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PPVQRIQMTRRQSVGRGLQL", "down_seq": "PGIGGMQQHFFDDEDRTVPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P28482-1", "kinase_gene_name": "MAPK1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "12594221", "url": "https://glygen.org/publication/PubMed/12594221" }, { "database": "PubMed", "id": "22028470", "url": "https://glygen.org/publication/PubMed/22028470" }, { "database": "PubMed", "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356" } ], "site_lbl": "Thr2116" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "site_lbl": "Thr2116" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2137.2137", "start_pos": 2137, "end_pos": 2137, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of novel ERK2 substrates through use of an engineered kinase and ATP analogs.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Eblen ST, Kumar NV, Shah K, Henderson MJ, Watts CK, Shokat KM, Weber MJ", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "12594221", "url": "https://glygen.org/publication/PubMed/12594221" } ] }, { "title": "Large-scale discovery of ERK2 substrates identifies ERK-mediated transcriptional regulation by ETV3.", "journal": "Science signaling", "date": "2011", "authors": "Carlson SM, Chouinard CR, Labadorf A, Lam CJ, Schmelzle K, Fraenkel E, White FM", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "22028470", "url": "https://glygen.org/publication/PubMed/22028470" } ] }, { "title": "Extracellular signal-regulated kinase 2 (ERK2) phosphorylation sites and docking domain on the nuclear pore complex protein Tpr cooperatively regulate ERK2-Tpr interaction.", "journal": "Molecular and cellular biology", "date": "2008", "authors": "Vomastek T, Iwanicki MP, Burack WR, Tiwari D, Kumar D, Parsons JT, Weber MJ, Nandicoori VK", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12594221", "url": "https://glygen.org/publication/PubMed/12594221", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22028470", "url": "https://glygen.org/publication/PubMed/22028470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PGIGGMQQHFFDDEDRTVPS", "down_seq": "PTLVVPHRTDGFAEAIHSPQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P28482-1", "kinase_gene_name": "MAPK1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "12594221", "url": "https://glygen.org/publication/PubMed/12594221" }, { "database": "PubMed", "id": "22028470", "url": "https://glygen.org/publication/PubMed/22028470" }, { "database": "PubMed", "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356" } ], "site_lbl": "Thr2137" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "site_lbl": "Thr2137" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P12270-1.2145.2145", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.2155.2155", "categories": [ "snv_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": 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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2175.2175", "start_pos": 2175, "end_pos": 2175, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SPQVAGVPRFRFGPPEDMPQ", "down_seq": "SSSHSDLGQLASQGGLGMYE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Thr2175" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P12270-1.2155.2155", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.2176.2176", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.2178.2178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.2180.2180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.2187.2187", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.2214.2214", "start_pos": 2214, "end_pos": 2214, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Extracellular signal-regulated kinase 2 (ERK2) phosphorylation sites and docking domain on the nuclear pore complex protein Tpr cooperatively regulate ERK2-Tpr interaction.", "journal": "Molecular and cellular biology", "date": "2008", "authors": "Vomastek T, Iwanicki MP, Burack WR, Tiwari D, Kumar D, Parsons JT, Weber MJ, Nandicoori VK", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YETPLFLAHEEESGGRSVPT", "down_seq": "PLQVAAPVTVFTESTTSDAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P28482-1", "kinase_gene_name": "MAPK1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18794356", "url": "https://glygen.org/publication/PubMed/18794356" } ], "site_lbl": "Thr2214" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "P12270-1.2228.2228", "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": "P12270-1.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "LQKHVEDLLTKLKEAKEQQA", "down_seq": "MEEKFHNELNAHIKLSNLYK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser270" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.379.379", "start_pos": 379, "end_pos": 379, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Phosphoproteomic analysis of distinct tumor cell lines in response to nocodazole treatment.", "journal": "Proteomics", "date": "2009", "authors": "Nagano K, Shinkawa T, Mutoh H, Kondoh O, Morimoto S, Inomata N, Ashihara M, Ishii N, Aoki Y, Haramura M", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLSATKRKGAILSEEELAAM", "down_seq": "PTAAAVAKIVKPGMKLTELY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "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": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ], "site_lbl": "Ser379" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P12270-1.381.381", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P12270-1.381.381", "start_pos": 381, "end_pos": 381, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SATKRKGAILSEEELAAMSP", "down_seq": "AAAVAKIVKPGMKLTELYNA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Thr381" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P12270-1.379.379", "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": "P12270-1.522.522", "start_pos": 522, "end_pos": 522, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Molecular cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VLLMELEEARGNHVIRDEEV", "down_seq": "SADISSSSEVISQHLVSYRN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser522" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P12270-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.525.525", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.527.527", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.529.529", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P12270-1.530.530", "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": "P12270-1.523.523", "start_pos": 523, "end_pos": 523, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLMELEEARGNHVIRDEEVS", "down_seq": "ADISSSSEVISQHLVSYRNI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser523" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P12270-1.522.522", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.525.525", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.527.527", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.529.529", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.530.530", "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": "P12270-1.527.527", "start_pos": 527, "end_pos": 527, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LEEARGNHVIRDEEVSSADI", "down_seq": "SSSEVISQHLVSYRNIEELQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser527" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P12270-1.522.522", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.525.525", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.529.529", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.530.530", "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": "P12270-1.528.528", "start_pos": 528, "end_pos": 528, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEARGNHVIRDEEVSSADIS", "down_seq": "SSEVISQHLVSYRNIEELQQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser528" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P12270-1.522.522", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P12270-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.525.525", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.527.527", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.529.529", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.530.530", "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": "P12270-1.529.529", "start_pos": 529, "end_pos": 529, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EARGNHVIRDEEVSSADISS", "down_seq": "SEVISQHLVSYRNIEELQQQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser529" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P12270-1.522.522", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P12270-1.525.525", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.527.527", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.530.530", "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": "P12270-1.530.530", "start_pos": 530, "end_pos": 530, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ARGNHVIRDEEVSSADISSS", "down_seq": "EVISQHLVSYRNIEELQQQN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser530" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P12270-1.522.522", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P12270-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P12270-1.525.525", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.527.527", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.529.529", "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": "P12270-1.62.62", "start_pos": 62, "end_pos": 62, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "RHEKFKVESEQQYFEIEKRL", "down_seq": "HSQERLVNETRECQSLRLEL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser62" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.632.632", "start_pos": 632, "end_pos": 632, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DMYRILLSQTTGVAIPLHAS", "down_seq": "LDDVSLASTPKRPSTSQTVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "site_lbl": "Ser632" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P12270-1.635.635", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P12270-1.641.641", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P12270-1.646.646", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P12270-1.650.650", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P12270-1.652.652", "categories": [ "glycosylation_flag", "snv_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": "P12270-1.641.641", "start_pos": 641, "end_pos": 641, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "TTGVAIPLHASSLDDVSLAS", "down_seq": "PKRPSTSQTVSTPAPVPVIE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr641" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P12270-1.632.632", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.635.635", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.646.646", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P12270-1.650.650", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P12270-1.652.652", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P12270-1.653.653", "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": "P12270-1.646.646", "start_pos": 646, "end_pos": 646, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "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": "IPLHASSLDDVSLASTPKRP", "down_seq": "TSQTVSTPAPVPVIESTEAI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser646" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P12270-1.632.632", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.635.635", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P12270-1.641.641", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.650.650", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.652.652", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P12270-1.653.653", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P12270-1.663.663", "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": "P12270-1.647.647", "start_pos": 647, "end_pos": 647, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "PLHASSLDDVSLASTPKRPS", "down_seq": "SQTVSTPAPVPVIESTEAIE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr647" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P12270-1.632.632", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P12270-1.635.635", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.641.641", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.646.646", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P12270-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P12270-1.650.650", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.652.652", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P12270-1.653.653", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P12270-1.663.663", "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": "P12270-1.648.648", "start_pos": 648, "end_pos": 648, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "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": "LHASSLDDVSLASTPKRPST", "down_seq": "QTVSTPAPVPVIESTEAIEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser648" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P12270-1.632.632", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.635.635", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P12270-1.641.641", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P12270-1.646.646", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P12270-1.650.650", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P12270-1.652.652", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P12270-1.653.653", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P12270-1.663.663", "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": "P12270-1.653.653", "start_pos": 653, "end_pos": 653, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LDDVSLASTPKRPSTSQTVS", "down_seq": "PAPVPVIESTEAIEAKAALK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr653" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P12270-1.635.635", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P12270-1.641.641", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P12270-1.646.646", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P12270-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P12270-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P12270-1.650.650", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P12270-1.652.652", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P12270-1.663.663", "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": "P12270-1.663.663", "start_pos": 663, "end_pos": 663, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "KRPSTSQTVSTPAPVPVIES", "down_seq": "EAIEAKAALKQLQEIFENYK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr663" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P12270-1.646.646", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P12270-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P12270-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P12270-1.650.650", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P12270-1.652.652", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P12270-1.653.653", "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": "P12270-1.740.740", "start_pos": 740, "end_pos": 740, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "FASKRYEMLQDNVEGYRREI", "down_seq": "SLHERNQKLTATTQKQEQII", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr740" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.849.849", "start_pos": 849, "end_pos": 849, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "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": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "P12270", "url": "https://www.iedb.org/epitope/P12270", "database": "IEDB", "categories": [ "Other" ] }, { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "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": "SETETKQRLSSQIEKLEHEI", "down_seq": "HLKKKLENEVEQRHTLTRNL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "P12270", "url": "https://www.iedb.org/epitope/P12270" }, { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Ser849" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "P12270-1.920.920", "start_pos": 920, "end_pos": 920, "uniprot_canonical_ac": "P12270-1", "length": 2363, "uniprot_id": "TPR_HUMAN", "protein_name": "Nucleoprotein TPR", "refseq_ac": "NP_003283", "refseq_name": "nucleoprotein TPR", "gene_name": "TPR", "gene_names_uniprotkb": "TPR", "gene_names_refseq": "MRT79; TPR", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.", "journal": "Science (New York, N.Y.)", "date": "2007", "authors": "Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ", "evidence": [ { "database": "UniProtKB", "id": "P12270", "url": "https://www.uniprot.org/uniprotkb/P12270" }, { "database": "iPTMnet", "id": "P12270-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270-1" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] } ], "crossref": [ { "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIATLKQHLSNMEVQVASQS", "down_seq": "QRTGKGQPSNKEDVDDLVSQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P12270", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P12270" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ], "site_lbl": "Ser920" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1275", "end_pos": "1275" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1812", "end_pos": "1812" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2061", "end_pos": "2061" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2187", "end_pos": "2187" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "458", "end_pos": "458" }, { "start_pos": "489", "end_pos": "489" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "2176", "end_pos": "2176" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1096", "end_pos": "1096" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1183", "end_pos": "1183" }, { "start_pos": "1204", "end_pos": "1204" }, { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1318", "end_pos": "1318" }, { "start_pos": "1394", "end_pos": "1394" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1470", "end_pos": "1470" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1658", "end_pos": "1658" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1662", "end_pos": "1662" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1690", "end_pos": "1690" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1698", "end_pos": "1698" }, { "start_pos": "1702", "end_pos": "1702" }, { "start_pos": "1707", "end_pos": "1707" }, { "start_pos": "1709", "end_pos": "1709" }, { "start_pos": "1710", "end_pos": "1710" }, { "start_pos": "1743", "end_pos": "1743" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1808", "end_pos": "1808" }, { "start_pos": "1822", "end_pos": "1822" }, { "start_pos": "1824", "end_pos": "1824" }, { "start_pos": "1837", "end_pos": "1837" }, { "start_pos": "1850", "end_pos": "1850" }, { "start_pos": "1985", "end_pos": "1985" }, { "start_pos": "2000", "end_pos": "2000" }, { "start_pos": "2043", "end_pos": "2043" }, { "start_pos": "2060", "end_pos": "2060" }, { "start_pos": "2063", "end_pos": "2063" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2074", "end_pos": "2074" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "2228", "end_pos": "2228" }, { "start_pos": "2316", "end_pos": "2316" }, { "start_pos": "2330", "end_pos": "2330" }, { "start_pos": "2331", "end_pos": "2331" }, { "start_pos": "2363", "end_pos": "2363" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "958", "end_pos": "958" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1185", "end_pos": "1185" }, { "start_pos": "1252", "end_pos": "1252" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "1385", "end_pos": "1385" }, { "start_pos": "1390", "end_pos": "1390" }, { "start_pos": "1398", "end_pos": "1398" }, { "start_pos": "1458", "end_pos": "1458" }, { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1462", "end_pos": "1462" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1692", "end_pos": "1692" }, { "start_pos": "1725", "end_pos": "1725" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1838", "end_pos": "1838" }, { "start_pos": "1839", "end_pos": "1839" }, { "start_pos": "1847", "end_pos": "1847" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "2034", "end_pos": "2034" }, { "start_pos": "2037", "end_pos": "2037" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2048", "end_pos": "2048" }, { "start_pos": "2050", "end_pos": "2050" }, { "start_pos": "2054", "end_pos": "2054" }, { "start_pos": "2073", "end_pos": "2073" }, { "start_pos": "2116", "end_pos": "2116" }, { "start_pos": "2137", "end_pos": "2137" }, { "start_pos": "2155", "end_pos": "2155" }, { "start_pos": "2175", "end_pos": "2175" }, { "start_pos": "2178", "end_pos": "2178" }, { "start_pos": "2180", "end_pos": "2180" }, { "start_pos": "2214", "end_pos": "2214" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "529", "end_pos": "529" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "653", "end_pos": "653" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "849", "end_pos": "849" }, { "start_pos": "920", "end_pos": "920" } ] } ], "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": "A2A368-1.13.13", "start_pos": 13, "end_pos": 13, "uniprot_canonical_ac": "A2A368-1", "length": 324, "uniprot_id": "MAGBG_HUMAN", "protein_name": "Melanoma-associated antigen B16", "refseq_ac": "NP_001093391", "refseq_name": "melanoma-associated antigen B16 isoform 1", "gene_name": "MAGEB16", "gene_names_uniprotkb": "MAGEB16", "gene_names_refseq": "MAGEB16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2A368", "url": "https://www.uniprot.org/uniprotkb/A2A368" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2A368", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MSQDQESPRCTH", "down_seq": "QHLQTFSETQSLEVAQVSKA", "snv": [ { "evidence": [ { "id": "A2A368", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368" } ], "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": "23", "chr_pos": "35802233", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D13", "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: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": "13", "end_pos": "13" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "A2A368-1.9.9", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "A2A368-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "A2A368-1", "length": 324, "uniprot_id": "MAGBG_HUMAN", "protein_name": "Melanoma-associated antigen B16", "refseq_ac": "NP_001093391", "refseq_name": "melanoma-associated antigen B16 isoform 1", "gene_name": "MAGEB16", "gene_names_uniprotkb": "MAGEB16", "gene_names_refseq": "MAGEB16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2A368", "url": "https://www.uniprot.org/uniprotkb/A2A368" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2A368", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KDFVKEKYLEYQQVANSDPA", "down_seq": "YEFLWGPRAKAETSKMKVLE", "snv": [ { "evidence": [ { "id": "A2A368", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "23", "chr_pos": "35803010", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R272", "keywords": [ "biomuta", "somatic", "cancer" ] }, { "evidence": [ { "id": "A2A368", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "35803011", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R272", "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: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": "13", "end_pos": "13" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "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": 1 } ], "sort_fields": [ "subjects_tested", "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": "A2A368-1.310.310", "start_pos": 310, "end_pos": 310, "uniprot_canonical_ac": "A2A368-1", "length": 324, "uniprot_id": "MAGBG_HUMAN", "protein_name": "Melanoma-associated antigen B16", "refseq_ac": "NP_001093391", "refseq_name": "melanoma-associated antigen B16 isoform 1", "gene_name": "MAGEB16", "gene_names_uniprotkb": "MAGEB16", "gene_names_refseq": "MAGEB16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2A368", "url": "https://www.uniprot.org/uniprotkb/A2A368" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2A368", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VLEFVAKVHGSYPHSFPSQY", "down_seq": "EALKEEEERARARI", "snv": [ { "evidence": [ { "id": "A2A368", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368" } ], "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": "23", "chr_pos": "35803125", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A310", "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: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": "13", "end_pos": "13" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "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": "A2A368-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "A2A368-1", "length": 324, "uniprot_id": "MAGBG_HUMAN", "protein_name": "Melanoma-associated antigen B16", "refseq_ac": "NP_001093391", "refseq_name": "melanoma-associated antigen B16 isoform 1", "gene_name": "MAGEB16", "gene_names_uniprotkb": "MAGEB16", "gene_names_refseq": "MAGEB16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2A368", "url": "https://www.uniprot.org/uniprotkb/A2A368" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2A368", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSSESDEASSNQEEEDSPSS", "down_seq": "EDTSDPRNVPADALDQKVAF", "snv": [ { "evidence": [ { "id": "A2A368", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "35802492", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S99", "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": "snv", "site_list": [ { "start_pos": "13", "end_pos": "13" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "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": "A2A368-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "A2A368-1", "length": 324, "uniprot_id": "MAGBG_HUMAN", "protein_name": "Melanoma-associated antigen B16", "refseq_ac": "NP_001093391", "refseq_name": "melanoma-associated antigen B16 isoform 1", "gene_name": "MAGEB16", "gene_names_uniprotkb": "MAGEB16", "gene_names_refseq": "MAGEB16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2A368", "url": "https://www.uniprot.org/uniprotkb/A2A368" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2A368", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MSQDQESP", "down_seq": "CTHDQHLQTFSETQSLEVAQ", "snv": [ { "evidence": [ { "id": "A2A368", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2A368" } ], "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": "23", "chr_pos": "35802221", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R9", "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": "snv", "site_list": [ { "start_pos": "13", "end_pos": "13" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "A2A368-1.13.13", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8NHJ6-1.233.233", "start_pos": 233, "end_pos": 233, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "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": "S", "start_aa": "S", "up_seq": "LELIVSGSLEDPRPSPTRSV", "down_seq": "TAAGPEDQPLMPTGSVPHSG", "glycosylation": [ { "glytoucan_ac": "G53434XO", "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": "Ser233", "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": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q8NHJ6-1.246.246", "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": "Q8NHJ6-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "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": "Q8NHJ6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSPTRSVSTAAGPEDQPLMP", "down_seq": "GSVPHSGLRRHWEVLIGVLV", "glycosylation": [ { "glytoucan_ac": "G29068FM", "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": "Thr246", "evidence": [ { "id": "30459171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30459171" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "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": "Thr246", "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": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "19", "chr_pos": "54665160", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T246", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8NHJ6-1.233.233", "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": 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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8NHJ6-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "FSIPSMTEDYAGRYRCYYRS", "down_seq": "VGWSQPSDPLELVMTGAYSK", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8NHJ6-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8NHJ6-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NHJ6-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NHJ6-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHJ6-1.112.112", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8NHJ6-1.113.113", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHJ6-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHJ6-1.122.122", "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": "Q8NHJ6-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "PSMTEDYAGRYRCYYRSPVG", "down_seq": "SQPSDPLELVMTGAYSKPTL", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "A", "comment": "Significant reduction in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NHJ6-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8NHJ6-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8NHJ6-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHJ6-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NHJ6-1.112.112", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHJ6-1.113.113", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NHJ6-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHJ6-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHJ6-1.122.122", "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": "Q8NHJ6-1.109.109", "start_pos": 109, "end_pos": 109, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TEDYAGRYRCYYRSPVGWSQ", "down_seq": "SDPLELVMTGAYSKPTLSAL", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NHJ6-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8NHJ6-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.112.112", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHJ6-1.113.113", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHJ6-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHJ6-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHJ6-1.122.122", "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": "Q8NHJ6-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DYAGRYRCYYRSPVGWSQPS", "down_seq": "PLELVMTGAYSKPTLSALPS", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NHJ6-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8NHJ6-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NHJ6-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHJ6-1.112.112", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.113.113", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8NHJ6-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHJ6-1.122.122", "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": "Q8NHJ6-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YAGRYRCYYRSPVGWSQPSD", "down_seq": "LELVMTGAYSKPTLSALPSP", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHJ6-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8NHJ6-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHJ6-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHJ6-1.113.113", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHJ6-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8NHJ6-1.122.122", "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": "Q8NHJ6-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "AGRYRCYYRSPVGWSQPSDP", "down_seq": "ELVMTGAYSKPTLSALPSPL", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8NHJ6-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHJ6-1.112.112", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHJ6-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NHJ6-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHJ6-1.122.122", "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": "Q8NHJ6-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GRYRCYYRSPVGWSQPSDPL", "down_seq": "LVMTGAYSKPTLSALPSPLV", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHJ6-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8NHJ6-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.112.112", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHJ6-1.113.113", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHJ6-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NHJ6-1.122.122", "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": "Q8NHJ6-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RSPVGWSQPSDPLELVMTGA", "down_seq": "SKPTLSALPSPLVTSGKSVT", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Significant reduction in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8NHJ6-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8NHJ6-1.112.112", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8NHJ6-1.113.113", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHJ6-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHJ6-1.122.122", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.139.139", "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": "Q8NHJ6-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPVGWSQPSDPLELVMTGAY", "down_seq": "KPTLSALPSPLVTSGKSVTL", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8NHJ6-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8NHJ6-1.112.112", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8NHJ6-1.113.113", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8NHJ6-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHJ6-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHJ6-1.139.139", "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": "Q8NHJ6-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SALPSPLVTSGKSVTLLCQS", "down_seq": "SPMDTFLLIKERAAHPLLHL", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8NHJ6-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.149.149", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHJ6-1.162.162", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHJ6-1.164.164", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.165.165", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NHJ6-1.167.167", "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": "Q8NHJ6-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LPSPLVTSGKSVTLLCQSRS", "down_seq": "MDTFLLIKERAAHPLLHLRS", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8NHJ6-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.147.147", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHJ6-1.162.162", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHJ6-1.164.164", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHJ6-1.165.165", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.167.167", "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": "Q8NHJ6-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LLCQSRSPMDTFLLIKERAA", "down_seq": "PLLHLRSEHGAQQHQAEFPM", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NHJ6-1.147.147", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8NHJ6-1.149.149", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.164.164", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.165.165", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHJ6-1.167.167", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NHJ6-1.170.170", "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": "Q8NHJ6-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "CQSRSPMDTFLLIKERAAHP", "down_seq": "LHLRSEHGAQQHQAEFPMSP", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHJ6-1.147.147", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8NHJ6-1.149.149", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.162.162", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHJ6-1.165.165", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.167.167", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NHJ6-1.170.170", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHJ6-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NHJ6-1.184.184", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHJ6-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "QSRSPMDTFLLIKERAAHPL", "down_seq": "HLRSEHGAQQHQAEFPMSPV", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.147.147", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8NHJ6-1.149.149", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.162.162", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHJ6-1.164.164", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.167.167", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHJ6-1.170.170", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHJ6-1.184.184", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHJ6-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "RSPMDTFLLIKERAAHPLLH", "down_seq": "RSEHGAQQHQAEFPMSPVTS", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NHJ6-1.147.147", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.149.149", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NHJ6-1.162.162", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.164.164", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.165.165", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.170.170", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHJ6-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHJ6-1.184.184", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHJ6-1.186.186", "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": "Q8NHJ6-1.170.170", "start_pos": 170, "end_pos": 170, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MDTFLLIKERAAHPLLHLRS", "down_seq": "HGAQQHQAEFPMSPVTSVHG", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8NHJ6-1.162.162", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NHJ6-1.164.164", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NHJ6-1.165.165", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.167.167", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHJ6-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NHJ6-1.184.184", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHJ6-1.186.186", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.188.188", "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": "Q8NHJ6-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PLLHLRSEHGAQQHQAEFPM", "down_seq": "PVTSVHGGTYRCFSSHGFSH", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHJ6-1.164.164", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.165.165", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8NHJ6-1.167.167", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8NHJ6-1.170.170", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHJ6-1.184.184", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.186.186", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHJ6-1.188.188", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHJ6-1.199.199", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHJ6-1.202.202", "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": "Q8NHJ6-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHJ6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LLHLRSEHGAQQHQAEFPMS", "down_seq": "VTSVHGGTYRCFSSHGFSHY", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "snv": [ { "evidence": [ { "id": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "54664381", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P184", "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: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": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NHJ6-1.164.164", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8NHJ6-1.165.165", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8NHJ6-1.167.167", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NHJ6-1.170.170", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHJ6-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.186.186", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHJ6-1.188.188", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHJ6-1.199.199", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHJ6-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.202.202", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHJ6-1.186.186", "start_pos": 186, "end_pos": 186, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HLRSEHGAQQHQAEFPMSPV", "down_seq": "SVHGGTYRCFSSHGFSHYLL", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHJ6-1.167.167", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8NHJ6-1.170.170", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.184.184", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.188.188", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHJ6-1.199.199", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHJ6-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHJ6-1.202.202", "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": "Q8NHJ6-1.188.188", "start_pos": 188, "end_pos": 188, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "RSEHGAQQHQAEFPMSPVTS", "down_seq": "HGGTYRCFSSHGFSHYLLSH", "mutagenesis": [ { "sequence_org": "V", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.170.170", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NHJ6-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NHJ6-1.184.184", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.186.186", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHJ6-1.199.199", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHJ6-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NHJ6-1.202.202", "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": "Q8NHJ6-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "EFPMSPVTSVHGGTYRCFSS", "down_seq": "GFSHYLLSHPSDPLELIVSG", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NHJ6-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8NHJ6-1.184.184", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8NHJ6-1.186.186", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8NHJ6-1.188.188", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.202.202", "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": "Q8NHJ6-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "PMSPVTSVHGGTYRCFSSHG", "down_seq": "SHYLLSHPSDPLELIVSGSL", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8NHJ6-1.184.184", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8NHJ6-1.186.186", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8NHJ6-1.188.188", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.199.199", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHJ6-1.202.202", "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": "Q8NHJ6-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSPVTSVHGGTYRCFSSHGF", "down_seq": "HYLLSHPSDPLELIVSGSLE", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHJ6-1.183.183", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.184.184", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8NHJ6-1.186.186", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NHJ6-1.188.188", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.199.199", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHJ6-1.201.201", "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": "Q8NHJ6-1.30.30", "start_pos": 30, "end_pos": 30, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "CLGLSLGPRTHMQAGPLPKP", "down_seq": "LWAEPGSVISWGNSVTIWCQ", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8NHJ6-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHJ6-1.35.35", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHJ6-1.41.41", "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": "Q8NHJ6-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LGPRTHMQAGPLPKPTLWAE", "down_seq": "GSVISWGNSVTIWCQGTLEA", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "Significant reduction in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NHJ6-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NHJ6-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NHJ6-1.41.41", "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": "Q8NHJ6-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "MQAGPLPKPTLWAEPGSVIS", "down_seq": "GNSVTIWCQGTLEAREYRLD", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8NHJ6-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NHJ6-1.35.35", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.59.59", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHJ6-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHJ6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ISWGNSVTIWCQGTLEAREY", "down_seq": "LDKEESPAPWDRQNPLEPKN", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "snv": [ { "evidence": [ { "id": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "54663859", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R59", "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: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": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.41.41", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHJ6-1.63.63", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHJ6-1.64.64", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NHJ6-1.65.65", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHJ6-1.66.66", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHJ6-1.68.68", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHJ6-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "NSVTIWCQGTLEAREYRLDK", "down_seq": "ESPAPWDRQNPLEPKNKARF", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8NHJ6-1.59.59", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHJ6-1.64.64", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.65.65", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.66.66", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHJ6-1.68.68", "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": "Q8NHJ6-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SVTIWCQGTLEAREYRLDKE", "down_seq": "SPAPWDRQNPLEPKNKARFS", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8NHJ6-1.59.59", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHJ6-1.63.63", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHJ6-1.65.65", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.66.66", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHJ6-1.68.68", "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": "Q8NHJ6-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VTIWCQGTLEAREYRLDKEE", "down_seq": "PAPWDRQNPLEPKNKARFSI", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8NHJ6-1.59.59", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.63.63", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHJ6-1.64.64", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHJ6-1.66.66", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHJ6-1.68.68", "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": "Q8NHJ6-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TIWCQGTLEAREYRLDKEES", "down_seq": "APWDRQNPLEPKNKARFSIP", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8NHJ6-1.59.59", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.63.63", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.64.64", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHJ6-1.65.65", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.68.68", "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": "Q8NHJ6-1.68.68", "start_pos": 68, "end_pos": 68, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "WCQGTLEAREYRLDKEESPA", "down_seq": "WDRQNPLEPKNKARFSIPSM", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8NHJ6-1.59.59", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NHJ6-1.63.63", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NHJ6-1.64.64", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHJ6-1.65.65", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.66.66", "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": "Q8NHJ6-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RQNPLEPKNKARFSIPSMTE", "down_seq": "YAGRYRCYYRSPVGWSQPSD", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8NHJ6-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NHJ6-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NHJ6-1.111.111", "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": "Q8NHJ6-1.95.95", "start_pos": 95, "end_pos": 95, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LEPKNKARFSIPSMTEDYAG", "down_seq": "YRCYYRSPVGWSQPSDPLEL", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8NHJ6-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHJ6-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHJ6-1.112.112", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.113.113", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHJ6-1.114.114", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHJ6-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.", "journal": "Nature", "date": "2018", "authors": "Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, Lu Z, Xie J, Churchill H, Xu Y, Zhou Z, Wu G, Yu C, John S, Hirayasu K, Nguyen N, Liu X, Huang F, Li L, Deng H, Tang H, Sadek AH, Zhang L, Huang T, Zou Y, Chen B, Zhu H, Arase H, Xia N, Jiang Y, Collins R, You MJ, Homsi J, Unni N, Lewis C, Chen GQ, Fu YX, Liao XC, An Z, Zheng J, Zhang N, Zhang CC", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PKNKARFSIPSMTEDYAGRY", "down_seq": "CYYRSPVGWSQPSDPLELVM", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "No significant change in APOE-mediated activation of LILRB4.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "30333625", "url": "https://glygen.org/publication/PubMed/30333625" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8NHJ6-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NHJ6-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHJ6-1.106.106", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHJ6-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NHJ6-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHJ6-1.112.112", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHJ6-1.113.113", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHJ6-1.114.114", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHJ6-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHJ6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2065157970", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2065157970", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2065157970", "url": "https://www.ensembl.org/id/rs2065157970", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2065157970", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2065157970", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAYSKPTLSALPSPLVTSGK", "down_seq": "VTLLCQSRSPMDTFLLIKER", "snv": [ { "evidence": [ { "id": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" }, { "id": "rs2065157970", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2065157970" }, { "id": "rs2065157970", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2065157970" }, { "id": "rs2065157970", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2065157970" } ], "glycoeffect": [ "n-glyco-sequon-gain", "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-gain (SVT->NVT).", "chr_id": "19", "chr_pos": "54664246", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S139", "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": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8NHJ6-1.122.122", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NHJ6-1.147.147", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8NHJ6-1.149.149", "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": "Q8NHJ6-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHJ6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MIPTFTALLCLGLSLGP", "down_seq": "THMQAGPLPKPTLWAEPGSV", "snv": [ { "evidence": [ { "id": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "19", "chr_pos": "54663551", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R18", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NHJ6-1.0.0", "categories": [ "biomarkers_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHJ6-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NHJ6-1.35.35", "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": 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": "Q8NHJ6-1.284.284", "start_pos": 284, "end_pos": 284, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHJ6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VLVVSILLLSLLLFLLLQHW", "down_seq": "QGKHRTLAQRQADFQRPPGA", "snv": [ { "evidence": [ { "id": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "54665907", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R284", "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: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: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": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "54665908", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R284", "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: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: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": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q8NHJ6-1.300.300", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q8NHJ6-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHJ6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LQHWRQGKHRTLAQRQADFQ", "down_seq": "PPGAAEPEPKDGGLQRRSSP", "snv": [ { "evidence": [ { "id": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "19", "chr_pos": "54666263", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R300", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NHJ6-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHJ6-1.319.319", "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": 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": "Q8NHJ6-1.334.334", "start_pos": 334, "end_pos": 334, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1400295853", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1400295853", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1400295853", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1400295853#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1400295853", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1400295853", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LQRRSSPAADVQGENFCAAV", "down_seq": "NTQPEDGVEMDTRQSPHDED", "snv": [ { "evidence": [ { "id": "rs1400295853", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1400295853" }, { "id": "rs1400295853", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1400295853#frequency_tab" }, { "id": "rs1400295853", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1400295853" } ], "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": "19", "chr_pos": "54666710", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K334", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NHJ6-1.319.319", "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": "Q8NHJ6-1.361.361", "start_pos": 361, "end_pos": 361, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHJ6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GVEMDTRQSPHDEDPQAVTY", "down_seq": "KVKHSRPRREMASPPSPLSG", "snv": [ { "evidence": [ { "id": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" } ], "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": "19", "chr_pos": "54667675", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A361", "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: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": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "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": "Q8NHJ6-1.407.407", "start_pos": 407, "end_pos": 407, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHJ6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KDRQAEEDRQMDTEAAASEA", "down_seq": "QDVTYAQLHSFTLRQKATEP", "snv": [ { "evidence": [ { "id": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" } ], "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 (6).", "chr_id": "19", "chr_pos": "54667891", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P407", "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: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: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: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: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": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8NHJ6-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHJ6-1.423.423", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8NHJ6-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHJ6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RQAEEDRQMDTEAAASEAPQ", "down_seq": "VTYAQLHSFTLRQKATEPPP", "snv": [ { "evidence": [ { "id": "Q8NHJ6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHJ6" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DVT->NVT).", "chr_id": "19", "chr_pos": "54667897", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D409", "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": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8NHJ6-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NHJ6-1.423.423", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8NHJ6-1.423.423", "start_pos": 423, "end_pos": 423, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747881421", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747881421", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747881421", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747881421", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747881421", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747881421", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ASEAPQDVTYAQLHSFTLRQ", "down_seq": "ATEPPPSQEGASPAEPSVYA", "snv": [ { "evidence": [ { "id": "rs747881421", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747881421" }, { "id": "rs747881421", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747881421" }, { "id": "rs747881421", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747881421" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KAT->NAT).", "chr_id": "19", "chr_pos": "54667941", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K423", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NHJ6-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NHJ6-1.409.409", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHJ6-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "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": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "iPTMnet", "id": "Q8NHJ6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHJ6" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHJ6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHJ6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QRPPGAAEPEPKDGGLQRRS", "down_seq": "PAADVQGENFCAAVKNTQPE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q8NHJ6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHJ6" } ], "site_lbl": "Ser319" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHJ6-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHJ6-1.334.334", "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": "Q8NHJ6-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q8NHJ6-1", "length": 448, "uniprot_id": "LIRB4_HUMAN", "protein_name": "Leukocyte immunoglobulin-like receptor subfamily B member 4", "refseq_ac": "NP_001265356", "refseq_name": "leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor", "gene_name": "LILRB4", "gene_names_uniprotkb": "LILRB4; ILT3; LIR5", "gene_names_refseq": "B4; CD85K; ILT-3; ILT3; LILRB4; LIR-5; LIR5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHJ6", "url": "https://www.uniprot.org/uniprotkb/Q8NHJ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteomic blood profiling in mild, severe and critical COVID-19 patients.", "journal": "Scientific reports", "date": "2021-03-18", "authors": "Patel Hamel, Ashton Nicholas J, Dobson Richard J B, Andersson Lars-Magnus, Yilmaz Aylin, Blennow Kaj, Gisslen Magnus, Zetterberg Henrik", "evidence": [ { "database": "BiomarkerKB", "id": "AN6423-1", "url": "https://biomarkerkb.org/biomarker/AN6423-1" } ], "reference": [ { "type": "PubMed", "id": "33737684", "url": "https://glygen.org/publication/PubMed/33737684" } ] } ], "crossref": [ { "id": "AN6423-1", "url": "https://biomarkerkb.org/biomarker/AN6423-1", "database": "BiomarkerKB", "categories": [ "Biomarkers" ] }, { "id": "33737684", "url": "https://glygen.org/publication/PubMed/33737684", "database": "PubMed", "categories": [ "Other" ] } ], "biomarkers": [ { "biomarker_id": "AN6423-1", "biomarker_canonical_id": "AN6423", "best_biomarker_role": [ "prognostic" ], "condition": { "id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a subtype of Betacoronavirus pandemicum." }, "name_list": [ "COVID-19", "2019 Novel Coronavirus (2019-nCoV)", "2019-nCoV infection", "COVID19", "SARS-CoV-2 infection", "2019 novel coronavirus infection", "coronavirus disease 2019", "severe acute respiratory syndrome coronavirus 2 infectious disease", "2019 novel coronavirus", "2019-nCoV", "SARS-CoV-2", "SARS-coronavirus 2", "beta-CoV", "beta-CoVs", "betacoronavirus", "severe acute respiratory syndrome coronavirus 2", "-CoV", "-CoVs", "-coronavirus" ], "id_list": [ "DOID:0080600", "MONDO:0100096" ] }, "evidence": [ { "id": "AN6423-1", "database": "BiomarkerKB", "url": "https://biomarkerkb.org/biomarker/AN6423-1" }, { "id": "33737684", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33737684" } ], "assessed_biomarker_entity": [ "Leukocyte immunoglobulin-like receptor subfamily B member 4" ], "biomarker": [ "increased LILRB4 level" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "233", "end_pos": "233" }, { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "snv", "site_list": [ { "start_pos": "139", "end_pos": "139" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "319", "end_pos": "319" } ] } ], "categories": [ "biomarkers_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q8NHJ6-1.18.18", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "O75391-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" }, { "database": "O-GlcNAc Atlas", "id": "O75391", "url": "https://oglcnac.org/atlas/detail/O75391" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins.", "journal": "Cell reports", "date": "2022-06-14", "authors": "Xu Senhan, Tong Ming, Suttapitugsakul Suttipong, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "O75391", "url": "https://oglcnac.org/atlas/detail/O75391" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391", "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": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75391", "url": "https://oglcnac.org/atlas/detail/O75391", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AMNEIRAKKRLRQSGEELPP", "down_seq": "", "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": "Thr226", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "O75391", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" }, { "id": "O75391", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O75391" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O75391-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O75391-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75391-1.227.227", "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": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75391-1.227.227", "start_pos": 227, "end_pos": 227, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" }, { "database": "O-GlcNAc Atlas", "id": "O75391", "url": "https://oglcnac.org/atlas/detail/O75391" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "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": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391", "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": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75391", "url": "https://oglcnac.org/atlas/detail/O75391", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs772412987", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772412987", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772412987", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772412987", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772412987", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772412987#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772412987", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772412987", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MNEIRAKKRLRQSGEELPPT", "down_seq": "", "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": "Ser227", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "O75391", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75391" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "O75391", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O75391" } ] } ], "snv": [ { "evidence": [ { "id": "rs772412987", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772412987" }, { "id": "rs772412987", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772412987" }, { "id": "rs772412987", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772412987#frequency_tab" }, { "id": "rs772412987", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772412987" } ], "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": "17", "chr_pos": "4959539", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S227", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75391-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O75391-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75391-1.226.226", "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75391-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750918890", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750918890", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750918890", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750918890", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750918890", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750918890", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DAAHMLQANKTYGCVPVANK", "down_seq": "DTRSIEEAMNEIRAKKRLRQ", "snv": [ { "evidence": [ { "id": "rs750918890", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750918890" }, { "id": "rs750918890", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750918890" }, { "id": "rs750918890", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750918890" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKR->NKT).", "chr_id": "17", "chr_pos": "4959625", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R198", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "O75391-1.202.202", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75391-1.207.207", "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": "O75391-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "KTYGCVPVANKRDTRSIEEA", "down_seq": "NEIRAKKRLRQSGEELPPTS", "snv": [ { "evidence": [ { "id": "O75391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "4959597", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "M207", "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": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O75391-1.198.198", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O75391-1.202.202", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O75391-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O75391-1.226.226", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75391-1.227.227", "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": "O75391-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RSIEEAMNEIRAKKRLRQSG", "down_seq": "ELPPTS", "snv": [ { "evidence": [ { "id": "O75391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75391" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "17", "chr_pos": "4959557", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E221", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O75391-1.202.202", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "O75391-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O75391-1.226.226", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75391-1.227.227", "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": 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": "O75391-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DVVEVAGLTSFSFGEDDDCR", "down_seq": "VMIFKKEFAPSDEELDSYRR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Tyr103" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "O75391-1.114.114", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O75391-1.121.121", "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": "O75391-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "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": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391", "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": "SFGEDDDCRYVMIFKKEFAP", "down_seq": "DEELDSYRRGEEWDPQKAEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser114" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O75391-1.103.103", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O75391-1.121.121", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75391-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Tang LY, Deng N, Wang LS, Dai J, Wang ZL, Jiang XS, Li SJ, Li L, Sheng QH, Wu DQ, Li L, Zeng R", "evidence": [ { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "17693683", "url": "https://glygen.org/publication/PubMed/17693683" } ] } ], "crossref": [ { "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17693683", "url": "https://glygen.org/publication/PubMed/17693683", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "CRYVMIFKKEFAPSDEELDS", "down_seq": "RRGEEWDPQKAEEKRKLKEL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" }, { "database": "PubMed", "id": "17693683", "url": "https://glygen.org/publication/PubMed/17693683" } ], "site_lbl": "Tyr121" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O75391-1.103.103", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O75391-1.114.114", "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": "O75391-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "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": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKELAQRQEEEAAQQGPVVV", "down_seq": "PASDYKDKYSHLIGKGAAKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Ser158" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "O75391-1.161.161", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75391-1.161.161", "start_pos": 161, "end_pos": 161, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "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": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAQRQEEEAAQQGPVVVSPA", "down_seq": "DYKDKYSHLIGKGAAKDAAH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser161" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O75391-1.158.158", "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": "O75391-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "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": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MLQANKTYGCVPVANKRDTR", "down_seq": "IEEAMNEIRAKKRLRQSGEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "site_lbl": "Ser202" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O75391-1.198.198", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O75391-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O75391-1.221.221", "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": "O75391-1.57.57", "start_pos": 57, "end_pos": 57, "uniprot_canonical_ac": "O75391-1", "length": 227, "uniprot_id": "SPAG7_HUMAN", "protein_name": "Sperm-associated antigen 7", "refseq_ac": "NP_004881", "refseq_name": "sperm-associated antigen 7", "gene_name": "SPAG7", "gene_names_uniprotkb": "SPAG7", "gene_names_refseq": "ACRP; FSA-1; SPAG7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" } ], "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": "O75391", "url": "https://www.uniprot.org/uniprotkb/O75391" }, { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391", "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": "LQEQEKQQKVEFRKRMEKEV", "down_seq": "DFIQDSGQIKKKFQPMNKIE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75391" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser57" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "snv", "site_list": [ { "start_pos": "198", "end_pos": "198" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "227", "end_pos": "227" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "57", "end_pos": "57" } ] } ], "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": "P11150-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Role of N-linked glycosylation in the secretion and activity of endothelial lipase.", "journal": "Journal of lipid research", "date": "2004-11", "authors": "Miller Gwen C, Long Christopher J, Bojilova Ekaterina D, Marchadier Dawn, Badellino Karen O, Blanchard Nadine, Fuki Ilia V, Glick Jane M, Rader Daniel J", "evidence": [ { "database": "GlyGen", "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481" } ], "reference": [ { "type": "PubMed", "id": "15342690", "url": "https://glygen.org/publication/PubMed/15342690" } ] } ], "crossref": [ { "id": "15342690", "url": "https://glygen.org/publication/PubMed/15342690", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LENWIWQMVAALKSQPAQPV", "down_seq": "VGLVDWITLAHDHYTIAVRN", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "automatic_literature_mining", "site_category_dict": { "automatic_literature_mining": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn116", "evidence": [ { "id": "15342690", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/15342690" }, { "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": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "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", "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": 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", "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": "P11150-1.362.362", "start_pos": 362, "end_pos": 362, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "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": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1266590486", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1266590486", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1266590486", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1266590486", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VTRAQSPFKVYHYQFKIQFI", "down_seq": "QTETPIQTTFTMSLLGTKEK", "glycosylation": [ { "glytoucan_ac": "G00273SJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "G00912UN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "G43769HG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "G45504EY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "G86182NS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "IQFInQTETPIQTTFTMSLLGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn362", "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": "Asn362", "evidence": [ { "id": "P11150", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P11150#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1266590486", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1266590486" }, { "id": "rs1266590486", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1266590486" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NQT->SQT).", "chr_id": "15", "chr_pos": "58560897", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N362", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "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": 13 }, { "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": 12 }, { "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": 12 } ], "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": 12 }, { "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": 12 }, { "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": 12 } ], "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": "P11150-1.397.397", "start_pos": 397, "end_pos": 397, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LGTKEKMQKIPITLGKGIAS", "down_seq": "KTYSFLITLDVDIGELIMIK", "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": "Asn397", "evidence": [ { "id": "P11150", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P11150#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P11150-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P11150-1.399.399", "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": "P11150-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "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": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1458586455", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1458586455", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1458586455", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1458586455", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ALGQSLKPEPFGRRAQAVET", "down_seq": "KTLHEMKTRFLLFGETNQGC", "glycosylation": [ { "glytoucan_ac": "G00912UN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G07246CJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G07755XJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G10488MI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G14972EH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G17208MA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G46691LC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G68490OW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G83460ZZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G85282JO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "G92551JA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AQAVETnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn42", "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": "Asn42", "evidence": [ { "id": "P11150", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P11150#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1458586455", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1458586455" }, { "id": "rs1458586455", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1458586455" } ], "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": "15", "chr_pos": "58538370", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N42", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P11150-1.44.44", "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": 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": 19 }, { "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": 19 } ], "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": 19 }, { "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": 19 }, { "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": 19 } ], "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": "P11150-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs201177069", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201177069", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201177069", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201177069#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201177069", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201177069", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TNQGCQIRINHPDTLQECGF", "down_seq": "SSLPLVMIIHGWSVDGVLEN", "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": "Asn78", "evidence": [ { "id": "P11150", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P11150#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs201177069", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201177069" }, { "id": "rs201177069", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201177069#frequency_tab" }, { "id": "rs201177069", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201177069" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->SSS).", "chr_id": "15", "chr_pos": "58538477", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N78", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201177069", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201177069" }, { "id": "rs201177069", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201177069#frequency_tab" }, { "id": "rs201177069", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201177069" } ], "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": "15", "chr_pos": "58538477", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N78", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P11150-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P11150-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P11150-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P11150-1.95.95", "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": 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": "P11150-1.255.275", "start_pos": 255, "end_pos": 275, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Human hepatic and lipoprotein lipase: the loop covering the catalytic site mediates lipase substrate specificity.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Dugi KA, Dichek HL, Santamarina-Fojo S", "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "reference": [ { "type": "PubMed", "id": "7592706", "url": "https://glygen.org/publication/PubMed/7592706" } ] } ], "crossref": [ { "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7592706", "url": "https://glygen.org/publication/PubMed/7592706", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "HFLELYRHIAQHGFNAITQTI", "start_aa": "H", "up_seq": "KQPIGHYDFYPNGGSFQPGC", "down_seq": "KCSHERSVHLFIDSLLHAGT", "mutagenesis": [ { "sequence_org": "HFLELYRHIAQHGFNAITQTI", "sequence_mut": "NIGEAIRVIAERGLGDVDQLV", "comment": "Increased triglyceride hydrolase and reduced phospholipase activity.", "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" }, { "database": "PubMed", "id": "7592706", "url": "https://glygen.org/publication/PubMed/7592706" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "P11150-1.255.276", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P11150-1.282.282", "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": "P11150-1.255.276", "start_pos": 255, "end_pos": 276, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Human hepatic and lipoprotein lipase: the loop covering the catalytic site mediates lipase substrate specificity.", "journal": "The Journal of biological chemistry", "date": "1995", "authors": "Dugi KA, Dichek HL, Santamarina-Fojo S", "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "reference": [ { "type": "PubMed", "id": "7592706", "url": "https://glygen.org/publication/PubMed/7592706" } ] } ], "crossref": [ { "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7592706", "url": "https://glygen.org/publication/PubMed/7592706", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "HFLELYRHIAQHGFNAITQTIK", "start_aa": "H", "up_seq": "KQPIGHYDFYPNGGSFQPGC", "down_seq": "CSHERSVHLFIDSLLHAGTQ", "mutagenesis": [ { "sequence_org": "HFLELYRHIAQHGFNAITQTIK", "sequence_mut": "CFHLEYLRIHQAHGFNATIQTKI", "comment": "Loss of triglyceride hydrolase and phospholipase activity.", "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" }, { "database": "PubMed", "id": "7592706", "url": "https://glygen.org/publication/PubMed/7592706" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P11150-1.255.275", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P11150-1.282.282", "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": "P11150-1.138.138", "start_pos": 138, "end_pos": 138, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200324727", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200324727", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200324727", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200324727", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200324727", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200324727#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200324727", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200324727", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200324727", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200324727", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GLVDWITLAHDHYTIAVRNT", "down_seq": "LVGKEVAALLRWLEESVQLS", "snv": [ { "evidence": [ { "id": "rs200324727", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200324727" }, { "id": "rs200324727", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200324727" }, { "id": "rs200324727", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200324727#frequency_tab" }, { "id": "rs200324727", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200324727" }, { "id": "rs200324727", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200324727" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTR->NTC).", "chr_id": "15", "chr_pos": "58541923", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R138", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "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": "P11150-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201654179", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201654179", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201654179", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201654179", "database": "1000Genomes", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "MDTSPLCFSILLVLCIF", "down_seq": "QSSALGQSLKPEPFGRRAQA", "snv": [ { "evidence": [ { "id": "rs201654179", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201654179" }, { "id": "rs201654179", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201654179" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IQS->NQS).", "chr_id": "15", "chr_pos": "58432085", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "I18", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P11150-1.2.2", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P11150-1.282.282", "start_pos": 282, "end_pos": 282, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HIAQHGFNAITQTIKCSHER", "down_seq": "VHLFIDSLLHAGTQSMAYPC", "snv": [ { "evidence": [ { "id": "P11150", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "58548366", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S282", "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": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P11150-1.255.275", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P11150-1.255.276", "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": "P11150-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756169441", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756169441", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756169441", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756169441", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756169441", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756169441#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs756169441", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756169441", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "M", "down_seq": "TSPLCFSILLVLCIFIQSSA", "snv": [ { "evidence": [ { "id": "rs756169441", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756169441" }, { "id": "rs756169441", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756169441" }, { "id": "rs756169441", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756169441#frequency_tab" }, { "id": "rs756169441", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756169441" } ], "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": "15", "chr_pos": "58432036", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D2", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P11150-1.18.18", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P11150-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IDSLLHAGTQSMAYPCGDMN", "down_seq": "FSQGLCLSCKKGRCNTLGYH", "snv": [ { "evidence": [ { "id": "P11150", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150" } ], "glycoeffect": [ "n-glyco-sequon-gain", "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: n-glyco-sequon-gain (SFS->NFS).", "chr_id": "15", "chr_pos": "58548441", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S307", "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": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P11150-1.308.308", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "P11150-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1164951731", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1164951731", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1164951731", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1164951731#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1164951731", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1164951731", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "DSLLHAGTQSMAYPCGDMNS", "down_seq": "SQGLCLSCKKGRCNTLGYHV", "snv": [ { "evidence": [ { "id": "rs1164951731", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1164951731" }, { "id": "rs1164951731", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1164951731#frequency_tab" }, { "id": "rs1164951731", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1164951731" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSF->NSC).", "chr_id": "15", "chr_pos": "58548444", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F308", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P11150-1.307.307", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P11150-1.387.387", "start_pos": 387, "end_pos": 387, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PIQTTFTMSLLGTKEKMQKI", "down_seq": "ITLGKGIASNKTYSFLITLD", "snv": [ { "evidence": [ { "id": "P11150", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150" } ], "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 (3).", "chr_id": "15", "chr_pos": "58560971", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P387", "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": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P11150-1.397.397", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P11150-1.399.399", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "P11150-1.399.399", "start_pos": 399, "end_pos": 399, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs775308938", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775308938", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775308938", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775308938", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775308938", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775308938#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775308938", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775308938", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TKEKMQKIPITLGKGIASNK", "down_seq": "YSFLITLDVDIGELIMIKFK", "snv": [ { "evidence": [ { "id": "P11150", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150" }, { "id": "rs775308938", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775308938" }, { "id": "rs775308938", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775308938" }, { "id": "rs775308938", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775308938#frequency_tab" }, { "id": "rs775308938", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775308938" } ], "glycoeffect": [ "n-glyco-sequon-loss", "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: n-glyco-sequon-loss (NKT->NKM).", "chr_id": "15", "chr_pos": "58563531", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T399", "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: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": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P11150-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P11150-1.397.397", "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": "P11150-1.430.430", "start_pos": 430, "end_pos": 430, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs148510360", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148510360", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs148510360", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148510360#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs148510360", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148510360", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "IGELIMIKFKWENSAVWANV", "down_seq": "DTVQTIIPWSTGPRHSGLVL", "snv": [ { "evidence": [ { "id": "P11150", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "W", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NVW->NVC).", "chr_id": "15", "chr_pos": "58563625", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W430", "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" ] }, { "evidence": [ { "id": "rs148510360", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148510360" }, { "id": "rs148510360", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148510360#frequency_tab" }, { "id": "rs148510360", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148510360" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "W", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVW->NVS).", "chr_id": "15", "chr_pos": "58563624", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W430", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "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": 1 } ], "sort_fields": [ "subjects_tested", "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": "P11150-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs549763129", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549763129", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs549763129", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549763129", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs549763129", "url": "https://www.ncbi.nlm.nih.gov/snp/rs549763129#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs549763129", "url": "http://gnomad.broadinstitute.org/awesome?query=rs549763129", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs549763129", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs549763129", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GQSLKPEPFGRRAQAVETNK", "down_seq": "LHEMKTRFLLFGETNQGCQI", "snv": [ { "evidence": [ { "id": "P11150", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150" }, { "id": "rs549763129", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549763129" }, { "id": "rs549763129", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549763129" }, { "id": "rs549763129", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs549763129#frequency_tab" }, { "id": "rs549763129", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs549763129" }, { "id": "rs549763129", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs549763129" } ], "glycoeffect": [ "n-glyco-sequon-loss", "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: n-glyco-sequon-loss (NKT->NKM).", "chr_id": "15", "chr_pos": "58538375", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T44", "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: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": "rs549763129", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549763129" }, { "id": "rs549763129", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549763129" }, { "id": "rs549763129", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs549763129#frequency_tab" }, { "id": "rs549763129", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs549763129" } ], "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 (NKT->NKR).", "chr_id": "15", "chr_pos": "58538375", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T44", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P11150-1.42.42", "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": 1 } ], "sort_fields": [ "subjects_tested", "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": "P11150-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LHEMKTRFLLFGETNQGCQI", "down_seq": "INHPDTLQECGFNSSLPLVM", "snv": [ { "evidence": [ { "id": "P11150", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "15", "chr_pos": "58538437", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R65", "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" } ] }, { "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: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": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P11150-1.78.78", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P11150-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P11150-1.80.80", "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": "P11150-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1595931775", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595931775", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1595931775", "url": "https://www.ensembl.org/id/rs1595931775", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NQGCQIRINHPDTLQECGFN", "down_seq": "SLPLVMIIHGWSVDGVLENW", "snv": [ { "evidence": [ { "id": "rs1595931775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595931775" }, { "id": "rs1595931775", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1595931775" } ], "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 (NSS->NPS).", "chr_id": "15", "chr_pos": "58538479", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S79", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P11150-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P11150-1.78.78", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P11150-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P11150-1.95.95", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P11150-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs774521901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774521901", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774521901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774521901", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774521901", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774521901", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QGCQIRINHPDTLQECGFNS", "down_seq": "LPLVMIIHGWSVDGVLENWI", "snv": [ { "evidence": [ { "id": "P11150", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NSS->NSF).", "chr_id": "15", "chr_pos": "58538483", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S80", "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": "rs774521901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774521901" }, { "id": "rs774521901", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774521901" }, { "id": "rs774521901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774521901" } ], "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 (NSS->NSP).", "chr_id": "15", "chr_pos": "58538482", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S80", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P11150-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P11150-1.78.78", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P11150-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P11150-1.95.95", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P11150-1.95.95", "start_pos": 95, "end_pos": 95, "uniprot_canonical_ac": "P11150-1", "length": 499, "uniprot_id": "LIPC_HUMAN", "protein_name": "Hepatic triacylglycerol lipase", "refseq_ac": "NP_000227", "refseq_name": "hepatic triacylglycerol lipase precursor", "gene_name": "LIPC", "gene_names_uniprotkb": "LIPC; HTGL", "gene_names_refseq": "HDLCQ12; HL; HTGL; LIPC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P11150", "url": "https://www.uniprot.org/uniprotkb/P11150" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P11150", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "CGFNSSLPLVMIIHGWSVDG", "down_seq": "LENWIWQMVAALKSQPAQPV", "snv": [ { "evidence": [ { "id": "P11150", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P11150" } ], "glycoeffect": [], "subjects_tested": "606", "subjects_positive": "4", "frequency": "0.7", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "58541794", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V95", "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: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": "glycosylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "255", "end_pos": "275" }, { "start_pos": "255", "end_pos": "276" } ] }, { "type": "snv", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P11150-1.78.78", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P11150-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P11150-1.80.80", "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": "Q8NA19-1.381.381", "start_pos": 381, "end_pos": 381, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "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": "rs2060088585", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2060088585", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2060088585", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2060088585", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1342122192", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1342122192", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1342122192", "url": "https://www.ensembl.org/id/rs1342122192", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LEVPQRTNDLKILPGQAVCP", "down_seq": "PGCRGIGHIRGPRYSGHHSA", "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": "Thr381", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs2060088585", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2060088585" }, { "id": "rs2060088585", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2060088585" } ], "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": "18", "chr_pos": "6138251", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T381", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1342122192", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1342122192" }, { "id": "rs1342122192", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1342122192" } ], "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": "18", "chr_pos": "6138252", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T381", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "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" ] }, { "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": "Q8NA19-1.509.509", "start_pos": 509, "end_pos": 509, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A novel strategy for global mapping of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry identification.", "journal": "Talanta", "date": "2017", "authors": "Shen B, Zhang W, Shi Z, Tian F, Deng Y, Sun C, Wang G, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NA19", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NA19" } ], "reference": [ { "type": "PubMed", "id": "28411811", "url": "https://glygen.org/publication/PubMed/28411811" } ] }, { "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": "Q8NA19", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NA19" }, { "database": "O-GlcNAc Atlas", "id": "Q8NA19", "url": "https://oglcnac.org/atlas/detail/Q8NA19" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "28411811", "url": "https://glygen.org/publication/PubMed/28411811", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NA19", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NA19", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NA19", "url": "https://oglcnac.org/atlas/detail/Q8NA19", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs373941763", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373941763", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373941763", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373941763", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373941763", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373941763#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs373941763", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373941763", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs967956699", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs967956699", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs967956699", "url": "https://www.ncbi.nlm.nih.gov/snp/rs967956699#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs967956699", "url": "http://gnomad.broadinstitute.org/awesome?query=rs967956699", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GLEYSVEQAQQVLHQSVSMS", "down_seq": "VSAHPFRDLPLGREQHCKLL", "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": "Thr509", "evidence": [ { "id": "28411811", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28411811" }, { "id": "Q8NA19", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NA19" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q8NA19", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NA19" } ] } ], "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" }, { "id": "rs373941763", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373941763" }, { "id": "rs373941763", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373941763" }, { "id": "rs373941763", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373941763#frequency_tab" }, { "id": "rs373941763", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373941763" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); o-glyco-site-loss (T->M).", "chr_id": "18", "chr_pos": "5969508", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T509", "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", "ebi" ] }, { "evidence": [ { "id": "rs967956699", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs967956699" }, { "id": "rs967956699", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs967956699#frequency_tab" }, { "id": "rs967956699", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs967956699" } ], "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": "18", "chr_pos": "5969509", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T509", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q8NA19-1.516.516", "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": 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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NA19-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2047529284", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2047529284", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2047529284", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2047529284", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YRLRLHFDGYLSCYDFWTNA", "down_seq": "SPDIHPVGWCEKTKHELHIP", "snv": [ { "evidence": [ { "id": "rs2047529284", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2047529284" }, { "id": "rs2047529284", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2047529284" } ], "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": "18", "chr_pos": "6243360", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G132", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "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": "Q8NA19-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RKDKFVWMDYLKACKLQNAP", "down_seq": "KLFRNRSPNGPMSKEFQVGM", "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6241382", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K176", "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: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": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q8NA19-1.187.187", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8NA19-1.17.17", "start_pos": 17, "end_pos": 17, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MKQPNRKRKLNMDSKE", "down_seq": "LDQDGRLEQAEEEKKPKDST", "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" } ], "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": "18", "chr_pos": "6311576", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R17", "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: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: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": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8NA19-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NA19-1.35.35", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8NA19-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777228939", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777228939", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777228939", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777228939", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777228939", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777228939#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777228939", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777228939", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KACKLQNAPKKLFRNRSPNG", "down_seq": "MSKEFQVGMKLEAVDRKNPS", "snv": [ { "evidence": [ { "id": "rs777228939", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777228939" }, { "id": "rs777228939", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777228939" }, { "id": "rs777228939", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777228939#frequency_tab" }, { "id": "rs777228939", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777228939" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGP->NGS).", "chr_id": "18", "chr_pos": "6239866", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P187", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs777228939", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777228939" }, { "id": "rs777228939", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777228939" }, { "id": "rs777228939", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777228939#frequency_tab" }, { "id": "rs777228939", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777228939" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGP->NGT).", "chr_id": "18", "chr_pos": "6239866", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P187", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8NA19-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NA19-1.206.206", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q8NA19-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1191293851", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1191293851", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1191293851", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1191293851", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs377764109", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377764109", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377764109", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377764109", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs377764109", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377764109#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs377764109", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377764109", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "GPMSKEFQVGMKLEAVDRKN", "down_seq": "SLVCVATIADIVEDRLLVHF", "snv": [ { "evidence": [ { "id": "rs1191293851", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1191293851" }, { "id": "rs1191293851", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1191293851" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NLS).", "chr_id": "18", "chr_pos": "6239808", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P206", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs377764109", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377764109" }, { "id": "rs377764109", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377764109" }, { "id": "rs377764109", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377764109#frequency_tab" }, { "id": "rs377764109", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377764109" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NTS).", "chr_id": "18", "chr_pos": "6239809", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P206", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NA19-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NA19-1.221.221", "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": 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": "Q8NA19-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VDRKNPSLVCVATIADIVED", "down_seq": "LLVHFDNWDDSYDYWCDVNS", "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6239763", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R221", "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: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": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NA19-1.206.206", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8NA19-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QPNRKRKLNMDSKERLDQDG", "down_seq": "LEQAEEEKKPKDSTTPLSHV", "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6311559", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R23", "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: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: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": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8NA19-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NA19-1.35.35", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8NA19-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201451800", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201451800", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201451800", "url": "https://www.ensembl.org/id/rs201451800", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YWCDVNSPYVQPVGWCQENG", "down_seq": "TLIAPQGYPNPENFSWTEYL", "snv": [ { "evidence": [ { "id": "rs201451800", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201451800" }, { "id": "rs201451800", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs201451800" } ], "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": "18", "chr_pos": "6237983", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R255", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "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": "Q8NA19-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FKMRLPHGFLPNMKLEVVDK", "down_seq": "NPRLIRVATIVDVDDQRVKV", "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6213208", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R308", "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: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": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8NA19-1.314.314", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8NA19-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HGFLPNMKLEVVDKRNPRLI", "down_seq": "VATIVDVDDQRVKVHFDGWD", "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" } ], "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": "18", "chr_pos": "6213190", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R314", "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: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": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8NA19-1.308.308", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8NA19-1.355.355", "start_pos": 355, "end_pos": 355, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1354796706", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1354796706", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1354796706", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1354796706", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HKYDYWVEADSPDIHPIGWC", "down_seq": "VTGHPLEVPQRTNDLKILPG", "snv": [ { "evidence": [ { "id": "rs1354796706", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1354796706" }, { "id": "rs1354796706", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1354796706" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DVT->NVT).", "chr_id": "18", "chr_pos": "6171861", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D355", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "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": "Q8NA19-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1461941448", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1461941448", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1461941448", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1461941448", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KERLDQDGRLEQAEEEKKPK", "down_seq": "STTPLSHVPSAAAQGAWSWE", "snv": [ { "evidence": [ { "id": "rs1461941448", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1461941448" }, { "id": "rs1461941448", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1461941448" } ], "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": "18", "chr_pos": "6301927", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D35", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8NA19-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8NA19-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NA19-1.46.46", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NA19-1.412.412", "start_pos": 412, "end_pos": 412, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs190553144", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190553144", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs190553144", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs190553144", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs190553144", "url": "https://www.ncbi.nlm.nih.gov/snp/rs190553144#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs190553144", "url": "http://gnomad.broadinstitute.org/awesome?query=rs190553144", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GPRYSGHHSAFGCPYSDMNL", "down_seq": "KEATLHDRLREQTQANLESD", "snv": [ { "evidence": [ { "id": "rs190553144", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190553144" }, { "id": "rs190553144", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs190553144" }, { "id": "rs190553144", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs190553144#frequency_tab" }, { "id": "rs190553144", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs190553144" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLK->NLT).", "chr_id": "18", "chr_pos": "6093493", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000588697", "site_lbl": "K412", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8NA19-1.420.420", "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": "Q8NA19-1.420.420", "start_pos": 420, "end_pos": 420, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SAFGCPYSDMNLKKEATLHD", "down_seq": "LREQTQANLESDSSHSKSKS", "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "18", "chr_pos": "6093469", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R420", "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: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": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8NA19-1.412.412", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NA19-1.440.440", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8NA19-1.440.440", "start_pos": 440, "end_pos": 440, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765858574", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765858574", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765858574", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765858574", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765858574", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765858574#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs765858574", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765858574", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RLREQTQANLESDSSHSKSK", "down_seq": "LCSLNFNGKHEKVNSQPRLV", "snv": [ { "evidence": [ { "id": "rs765858574", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765858574" }, { "id": "rs765858574", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765858574" }, { "id": "rs765858574", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765858574#frequency_tab" }, { "id": "rs765858574", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765858574" } ], "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 (SLC->NLC).", "chr_id": "18", "chr_pos": "6093409", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S440", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NA19-1.420.420", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NA19-1.447.447", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NA19-1.447.447", "start_pos": 447, "end_pos": 447, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs372111918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372111918", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372111918", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs372111918", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs372111918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372111918", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372111918", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372111918#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372111918", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372111918", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs372111918", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs372111918", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ANLESDSSHSKSKSLCSLNF", "down_seq": "GKHEKVNSQPRLVQQAKCLK", "snv": [ { "evidence": [ { "id": "rs372111918", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372111918" }, { "id": "rs372111918", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs372111918" }, { "id": "rs372111918", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372111918" }, { "id": "rs372111918", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372111918#frequency_tab" }, { "id": "rs372111918", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372111918" }, { "id": "rs372111918", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs372111918" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NFN->NFS).", "chr_id": "18", "chr_pos": "6093388", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N447", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8NA19-1.440.440", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NA19-1.46.46", "start_pos": 46, "end_pos": 46, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QAEEEKKPKDSTTPLSHVPS", "down_seq": "AAQGAWSWEWYLKEQKAVAA", "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "6", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6264029", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A46", "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: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: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": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8NA19-1.35.35", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q8NA19-1.516.516", "start_pos": 516, "end_pos": 516, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QAQQVLHQSVSMSTVSAHPF", "down_seq": "DLPLGREQHCKLLPGVADIR", "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "5969488", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R516", "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": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8NA19-1.509.509", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NA19-1.536.536", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8NA19-1.536.536", "start_pos": 536, "end_pos": 536, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NA19", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RDLPLGREQHCKLLPGVADI", "down_seq": "ASQVARWTVDEVAEFVQSLL", "snv": [ { "evidence": [ { "id": "Q8NA19", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NA19" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "5969428", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R536", "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: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": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NA19-1.516.516", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q8NA19-1.615.615", "start_pos": 615, "end_pos": 615, "uniprot_canonical_ac": "Q8NA19-1", "length": 623, "uniprot_id": "LMBL4_HUMAN", "protein_name": "Lethal(3)malignant brain tumor-like protein 4", "refseq_ac": "NP_775735", "refseq_name": "lethal(3)malignant brain tumor-like protein 4 isoform 1", "gene_name": "L3MBTL4", "gene_names_uniprotkb": "L3MBTL4", "gene_names_refseq": "HsT1031; L3MBTL4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NA19", "url": "https://www.uniprot.org/uniprotkb/Q8NA19" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs772902775", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772902775", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772902775", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772902775", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772902775", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772902775#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772902775", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772902775", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LKIYNSILMFRHSQELPEED", "down_seq": "ASGQEVRG", "snv": [ { "evidence": [ { "id": "rs772902775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772902775" }, { "id": "rs772902775", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772902775" }, { "id": "rs772902775", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772902775#frequency_tab" }, { "id": "rs772902775", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772902775" } ], "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": "18", "chr_pos": "5956248", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I615", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "381", "end_pos": "381" }, { "start_pos": "509", "end_pos": "509" } ] }, { "type": "snv", "site_list": [ { "start_pos": "509", "end_pos": "509" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "615", "end_pos": "615" } ] } ], "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": "Q12912-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q12912-1", "length": 555, "uniprot_id": "IRAG2_HUMAN", "protein_name": "Inositol 1,4,5-triphosphate receptor associated 2", "refseq_ac": "NP_001191055", "refseq_name": "inositol 1,4,5-triphosphate receptor associated 2 isoform a", "gene_name": "IRAG2", "gene_names_uniprotkb": "IRAG2; JAW1; LRMP", "gene_names_refseq": "IRAG2; JAW1; LRMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q12912", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12912" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q12912", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12912" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q12912", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12912", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NIGNAGMVAGMENNDRFSRR", "down_seq": "SSWRILGSKQSEHRPSLPRF", "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": "Ser402", "evidence": [ { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "Q12912", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12912" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "344", "end_pos": "344" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "91", "end_pos": "91" } ] } ], "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q12912-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "Q12912-1", "length": 555, "uniprot_id": "IRAG2_HUMAN", "protein_name": "Inositol 1,4,5-triphosphate receptor associated 2", "refseq_ac": "NP_001191055", "refseq_name": "inositol 1,4,5-triphosphate receptor associated 2 isoform a", "gene_name": "IRAG2", "gene_names_uniprotkb": "IRAG2; JAW1; LRMP", "gene_names_refseq": "IRAG2; JAW1; LRMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" } ], "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": "YGEVKDGALDVKRQHKCPGP", "down_seq": "SGPSPGTNLSGCIRMNDDPS", "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": "Thr42", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "344", "end_pos": "344" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "91", "end_pos": "91" } ] } ], "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": "Q12912-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "Q12912-1", "length": 555, "uniprot_id": "IRAG2_HUMAN", "protein_name": "Inositol 1,4,5-triphosphate receptor associated 2", "refseq_ac": "NP_001191055", "refseq_name": "inositol 1,4,5-triphosphate receptor associated 2 isoform a", "gene_name": "IRAG2", "gene_names_uniprotkb": "IRAG2; JAW1; LRMP", "gene_names_refseq": "IRAG2; JAW1; LRMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q12912", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12912" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q12912", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12912" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q12912", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12912", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1244173730", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1244173730", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1244173730", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1244173730", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IRMNDDPSMEENGVERVCPE", "down_seq": "LLQSREYSSLPLPRHTSSTD", "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": "Ser75", "evidence": [ { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "Q12912", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12912" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "snv": [ { "evidence": [ { "id": "rs1244173730", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1244173730" }, { "id": "rs1244173730", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1244173730" } ], "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": "25079742", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S75", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "344", "end_pos": "344" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q12912-1.91.91", "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": 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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q12912-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "Q12912-1", "length": 555, "uniprot_id": "IRAG2_HUMAN", "protein_name": "Inositol 1,4,5-triphosphate receptor associated 2", "refseq_ac": "NP_001191055", "refseq_name": "inositol 1,4,5-triphosphate receptor associated 2 isoform a", "gene_name": "IRAG2", "gene_names_uniprotkb": "IRAG2; JAW1; LRMP", "gene_names_refseq": "IRAG2; JAW1; LRMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2140254065", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2140254065", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2140254065", "url": "https://www.ensembl.org/id/rs2140254065", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MYAKEHAELEELKQVLLQNE", "down_seq": "SFNPLEDDDDCQIKKRSASL", "snv": [ { "evidence": [ { "id": "rs2140254065", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2140254065" }, { "id": "rs2140254065", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2140254065" } ], "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": "12", "chr_pos": "25104044", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R344", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "344", "end_pos": "344" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "Q12912-1.363.363", "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": "Q12912-1.533.533", "start_pos": 533, "end_pos": 533, "uniprot_canonical_ac": "Q12912-1", "length": 555, "uniprot_id": "IRAG2_HUMAN", "protein_name": "Inositol 1,4,5-triphosphate receptor associated 2", "refseq_ac": "NP_001191055", "refseq_name": "inositol 1,4,5-triphosphate receptor associated 2 isoform a", "gene_name": "IRAG2", "gene_names_uniprotkb": "IRAG2; JAW1; LRMP", "gene_names_refseq": "IRAG2; JAW1; LRMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139848797", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139848797", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139848797", "url": "https://www.ensembl.org/id/rs2139848797", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FLTGQLFQKSVDAAPTQQED", "down_seq": "WTSLEHILWPFTRLRHNGPP", "snv": [ { "evidence": [ { "id": "rs2139848797", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139848797" }, { "id": "rs2139848797", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139848797" } ], "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 (SWT->NWT).", "chr_id": "12", "chr_pos": "25032324", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S533", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "344", "end_pos": "344" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "424", "end_pos": "424" }, { "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": "Q12912-1.363.363", "start_pos": 363, "end_pos": 363, "uniprot_canonical_ac": "Q12912-1", "length": 555, "uniprot_id": "IRAG2_HUMAN", "protein_name": "Inositol 1,4,5-triphosphate receptor associated 2", "refseq_ac": "NP_001191055", "refseq_name": "inositol 1,4,5-triphosphate receptor associated 2 isoform a", "gene_name": "IRAG2", "gene_names_uniprotkb": "IRAG2; JAW1; LRMP", "gene_names_refseq": "IRAG2; JAW1; LRMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" } ], "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": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" }, { "database": "iPTMnet", "id": "Q12912", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q12912" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q12912", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q12912", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ERSFNPLEDDDDCQIKKRSA", "down_seq": "LNSKPSSLRRVTIASLPRNI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q12912", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q12912" } ], "site_lbl": "Ser363" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "344", "end_pos": "344" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q12912-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q12912-1.370.370", "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": "Q12912-1.370.370", "start_pos": 370, "end_pos": 370, "uniprot_canonical_ac": "Q12912-1", "length": 555, "uniprot_id": "IRAG2_HUMAN", "protein_name": "Inositol 1,4,5-triphosphate receptor associated 2", "refseq_ac": "NP_001191055", "refseq_name": "inositol 1,4,5-triphosphate receptor associated 2 isoform a", "gene_name": "IRAG2", "gene_names_uniprotkb": "IRAG2; JAW1; LRMP", "gene_names_refseq": "IRAG2; JAW1; LRMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" } ], "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": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" }, { "database": "iPTMnet", "id": "Q12912", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q12912" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Pre-fractionation Extends but also Creates a Bias in the Detectable HLA Class \u0399 Ligandome.", "journal": "Journal of proteome research", "date": "2019-04-05", "authors": "Demmers Laura C, Heck Albert J R, Wu Wei", "evidence": [ { "database": "iPTMnet", "id": "Q12912", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q12912" } ], "reference": [ { "type": "PubMed", "id": "30784271", "url": "https://glygen.org/publication/PubMed/30784271" } ] } ], "crossref": [ { "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q12912", "url": "https://www.iedb.org/epitope/Q12912", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q12912", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q12912", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "30784271", "url": "https://glygen.org/publication/PubMed/30784271", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EDDDDCQIKKRSASLNSKPS", "down_seq": "LRRVTIASLPRNIGNAGMVA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "IEDB", "id": "Q12912", "url": "https://www.iedb.org/epitope/Q12912" }, { "database": "iPTMnet", "id": "Q12912", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q12912" }, { "database": "PubMed", "id": "30784271", "url": "https://glygen.org/publication/PubMed/30784271" } ], "site_lbl": "Ser370" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "344", "end_pos": "344" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q12912-1.363.363", "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": "Q12912-1.424.424", "start_pos": 424, "end_pos": 424, "uniprot_canonical_ac": "Q12912-1", "length": 555, "uniprot_id": "IRAG2_HUMAN", "protein_name": "Inositol 1,4,5-triphosphate receptor associated 2", "refseq_ac": "NP_001191055", "refseq_name": "inositol 1,4,5-triphosphate receptor associated 2 isoform a", "gene_name": "IRAG2", "gene_names_uniprotkb": "IRAG2; JAW1; LRMP", "gene_names_refseq": "IRAG2; JAW1; LRMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SWRILGSKQSEHRPSLPRFI", "down_seq": "TYSWADAEEEKCELKTKDDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" } ], "site_lbl": "Ser424" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "344", "end_pos": "344" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "424", "end_pos": "424" }, { "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": "Q12912-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "Q12912-1", "length": 555, "uniprot_id": "IRAG2_HUMAN", "protein_name": "Inositol 1,4,5-triphosphate receptor associated 2", "refseq_ac": "NP_001191055", "refseq_name": "inositol 1,4,5-triphosphate receptor associated 2 isoform a", "gene_name": "IRAG2", "gene_names_uniprotkb": "IRAG2; JAW1; LRMP", "gene_names_refseq": "IRAG2; JAW1; LRMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" } ], "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": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" }, { "database": "iPTMnet", "id": "Q12912", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q12912" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q12912", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q12912", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VCPESLLQSREYSSLPLPRH", "down_seq": "SSTDGTITSSDPGLEILNMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q12912", "url": "https://www.uniprot.org/uniprotkb/Q12912" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q12912", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q12912" } ], "site_lbl": "Thr91" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "344", "end_pos": "344" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "75", "end_pos": "75" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "363", "end_pos": "363" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q12912-1.75.75", "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": "Q96A59-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "Q96A59-1", "length": 401, "uniprot_id": "MALD3_HUMAN", "protein_name": "MARVEL domain-containing protein 3", "refseq_ac": "NP_001017967", "refseq_name": "MARVEL domain-containing protein 3 isoform 1", "gene_name": "MARVELD3", "gene_names_uniprotkb": "MARVELD3; MRVLDC3", "gene_names_refseq": "MARVD3; MARVELD3; MRVLDC3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96A59", "url": "https://www.uniprot.org/uniprotkb/Q96A59" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96A59", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96A59", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DPRRKRSSDGNRRRDGDRDP", "down_seq": "RDQERDGNRDRNRDRERERE", "snv": [ { "evidence": [ { "id": "Q96A59", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96A59" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "71626407", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E60", "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: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: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": "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": "Q06413-1.150.150", "start_pos": 150, "end_pos": 150, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia.", "journal": "Cancer immunology research", "date": "2017", "authors": "Malaker SA, Penny SA, Steadman LG, Myers PT, Loke JC, Raghavan M, Bai DL, Shabanowitz J, Hunt DF, Cobbold M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" }, { "database": "O-GlcNAc Atlas", "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413" } ], "reference": [ { "type": "PubMed", "id": "28314751", "url": "https://glygen.org/publication/PubMed/28314751" } ] }, { "title": "Extended O-GlcNAc on HLA Class-I-Bound Peptides.", "journal": "Journal of the American Chemical Society", "date": "2015", "authors": "Marino F, Bern M, Mommen GPM, Leney AC, van Gaans-van den Brink JAM, Bonvin AMJJ, Becker C, van Els CACM, Heck AJR", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413" } ], "reference": [ { "type": "PubMed", "id": "26280087", "url": "https://glygen.org/publication/PubMed/26280087" } ] }, { "title": "The HLA Ligandome Comprises a Limited Repertoire of O-GlcNAcylated Antigens Preferentially Associated With HLA-B*07:02.", "journal": "Frontiers in immunology", "date": "2021", "authors": "Mukherjee S, Sanchez-Bernabeu A, Demmers LC, Wu W, Heck AJR", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413" } ], "reference": [ { "type": "PubMed", "id": "34925382", "url": "https://glygen.org/publication/PubMed/34925382" } ] } ], "crossref": [ { "id": "28314751", "url": "https://glygen.org/publication/PubMed/28314751", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "26280087", "url": "https://glygen.org/publication/PubMed/26280087", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34925382", "url": "https://glygen.org/publication/PubMed/34925382", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1581752987", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1581752987", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1581752987", "url": "https://www.ensembl.org/id/rs1581752987", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RQRLCAVPPPNFEMPVSIPV", "down_seq": "SHNSLVYSNPVSSLGNPNLL", "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": "Ser150", "evidence": [ { "id": "28314751", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28314751" }, { "id": "Q06413", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q06413" }, { "id": "26280087", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26280087" }, { "id": "34925382", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34925382" } ] } ], "snv": [ { "evidence": [ { "id": "rs1581752987", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1581752987" }, { "id": "rs1581752987", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1581752987" } ], "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": "5", "chr_pos": "88751998", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S150", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q06413-1.151.151", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q06413-1.152.152", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.151.151", "start_pos": 151, "end_pos": 151, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia.", "journal": "Cancer immunology research", "date": "2017", "authors": "Malaker SA, Penny SA, Steadman LG, Myers PT, Loke JC, Raghavan M, Bai DL, Shabanowitz J, Hunt DF, Cobbold M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" }, { "database": "O-GlcNAc Atlas", "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413" } ], "reference": [ { "type": "PubMed", "id": "28314751", "url": "https://glygen.org/publication/PubMed/28314751" } ] } ], "crossref": [ { "id": "28314751", "url": "https://glygen.org/publication/PubMed/28314751", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs937519642", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs937519642", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs937519642", "url": "https://www.ncbi.nlm.nih.gov/snp/rs937519642#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs937519642", "url": "http://gnomad.broadinstitute.org/awesome?query=rs937519642", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QRLCAVPPPNFEMPVSIPVS", "down_seq": "HNSLVYSNPVSSLGNPNLLP", "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": "Ser151", "evidence": [ { "id": "28314751", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28314751" }, { "id": "Q06413", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q06413" } ] } ], "snv": [ { "evidence": [ { "id": "rs937519642", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs937519642" }, { "id": "rs937519642", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs937519642#frequency_tab" }, { "id": "rs937519642", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs937519642" } ], "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": "5", "chr_pos": "88751994", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S151", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q06413-1.150.150", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q06413-1.152.152", "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": "Q06413-1.222.222", "start_pos": 222, "end_pos": 222, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "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": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" }, { "database": "O-GlcNAc Atlas", "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia.", "journal": "Cancer immunology research", "date": "2017", "authors": "Malaker SA, Penny SA, Steadman LG, Myers PT, Loke JC, Raghavan M, Bai DL, Shabanowitz J, Hunt DF, Cobbold M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" }, { "database": "O-GlcNAc Atlas", "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413" } ], "reference": [ { "type": "PubMed", "id": "28314751", "url": "https://glygen.org/publication/PubMed/28314751" } ] }, { "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": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "MEF2C Phosphorylation Is Required for Chemotherapy Resistance in Acute Myeloid Leukemia.", "journal": "Cancer discovery", "date": "2018", "authors": "Brown FC, Still E, Koche RP, Yim CY, Takao S, Cifani P, Reed C, Gunasekera S, Ficarro SB, Romanienko P, Mark W, McCarthy C, de Stanchina E, Gonen M, Seshan V, Bhola P, O'Donnell C, Spitzer B, Stutzke C, Lavallee VP, Hebert J, Krivtsov AV, Melnick A, Paietta EM, Tallman MS, Letai A, Sauvageau G, Pouliot G, Levine R, Marto JA, Armstrong SA, Kentsis A", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "29431698", "url": "https://glygen.org/publication/PubMed/29431698" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28314751", "url": "https://glygen.org/publication/PubMed/28314751", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2547087357", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2547087357", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2547087357", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2547087357", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29431698", "url": "https://glygen.org/publication/PubMed/29431698", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GDLTSGAGTSAGNGYGNPRN", "down_seq": "PGLLVSPGNLNKNMQAKSPP", "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": "Ser222", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q06413", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "28314751", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28314751" }, { "id": "Q06413", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q06413" } ] } ], "snv": [ { "evidence": [ { "id": "rs2547087357", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2547087357" }, { "id": "rs2547087357", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2547087357" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "5", "chr_pos": "88731875", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S222", "disease": [ { "disease_id": "DOID:0070050", "recommended_name": { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "An autosomal dominant intellectual developmental disorder that is characterized by global developmental delay with hypotonia, poor motor development with limited walking, impaired intellectual development with poor or absent speech, and behavioral abnormalities and that has_material_basis_in an autosomal dominant mutation of the MEF2C gene on chromosome 5q14.3." }, "synonyms": [ { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "MRD20", "description": "" }, { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "mental retardation, autosomal dominant 20", "description": "" }, { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "autosomal dominant mental retardation 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "Any autosomal dominant non-syndromic intellectual disability in which the cause of the disease is a mutation in the MEF2C gene." }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C Deficiency", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C autosomal dominant non-syndromic intellectual disability", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C haploinsufficiency syndrome (MCHS)", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C-related neurodevelopmental disorder", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C-related syndrome", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MRD20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "autosomal dominant non-syndromic intellectual disability caused by mutation in MEF2C", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "intellectual disability, autosomal dominant 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "intellectual disability, autosomal dominant type 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, autosomal dominant 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, autosomal dominant type 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, stereotypic movements, epilepsy, and/or cerebral malformations", "description": "" }, { "id": "MIM:613443", "resource": "MIM", "url": "https://www.omim.org/entry/613443", "name": "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language" } ], "unlinked_id_list": [], "evidence": [ { "id": "613443", "database": "MIM", "url": "https://www.omim.org/entry/613443" }, { "id": "0070050", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0070050" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "29431698", "url": "https://glygen.org/publication/PubMed/29431698" } ], "site_lbl": "Ser222" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q06413-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q06413-1.228.228", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q06413-1.234.234", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q06413-1.239.239", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q06413-1.240.240", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "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": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" }, { "database": "O-GlcNAc Atlas", "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "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": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia.", "journal": "Cancer immunology research", "date": "2017", "authors": "Malaker SA, Penny SA, Steadman LG, Myers PT, Loke JC, Raghavan M, Bai DL, Shabanowitz J, Hunt DF, Cobbold M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" }, { "database": "O-GlcNAc Atlas", "id": "Q06413", "url": "https://oglcnac.org/atlas/detail/Q06413" } ], "reference": [ { "type": "PubMed", "id": "28314751", "url": "https://glygen.org/publication/PubMed/28314751" } ] }, { "title": "Alternative pre-mRNA splicing governs expression of a conserved acidic transactivation domain in myocyte enhancer factor 2 factors of striated muscle and brain.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Zhu B, Ramachandran B, Gulick T", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "RefSeq", "id": "NP_001124477", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001124477" } ], "reference": [ { "type": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28314751", "url": "https://glygen.org/publication/PubMed/28314751", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1337373823", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1337373823", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1337373823", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1337373823#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1337373823", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1337373823", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RKPDLRVLIPPGSKNTMPSV", "down_seq": "EDVDLLLNQRINNSQSAQSL", "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": "Ser271", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q06413", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06413" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "28314751", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28314751" } ] } ], "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "No effect on transcriptional activation.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] } ], "snv": [ { "evidence": [ { "id": "rs1337373823", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1337373823" }, { "id": "rs1337373823", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1337373823#frequency_tab" }, { "id": "rs1337373823", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1337373823" } ], "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": "5", "chr_pos": "88730234", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S271", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q06413-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q06413-1.252.252", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q06413-1.264.264", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q06413-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q06413-1.272.272", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q06413-1.273.273", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q06413-1.275.275", "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": 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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Myocyte enhancer factor 2 acetylation by p300 enhances its DNA binding activity, transcriptional activity, and myogenic differentiation.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Ma K, Chan JK, Zhu G, Wu Z", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "reference": [ { "type": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "CDSPDPDADDSVGHSPESED", "down_seq": "YRKINEDIDLMISRQRLCAV", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Reduced acetylation. Further reduction in acetylation; when associated with R-119. Complete loss of acetylation, 15% less transactivation activity and slightly reduced DNA binding; when associated with R-119; R-234; R-239; R-252 and R-262.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q06413-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q06413-1.106.106", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q06413-1.110.110", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q06413-1.119.119", "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": "Q06413-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Myocyte enhancer factor 2 acetylation by p300 enhances its DNA binding activity, transcriptional activity, and myogenic differentiation.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Ma K, Chan JK, Zhu G, Wu Z", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "reference": [ { "type": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PDPDADDSVGHSPESEDKYR", "down_seq": "INEDIDLMISRQRLCAVPPP", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Reduced acetylation. Further reduction in acetylation; when associated with R-119. Complete loss of acetylation, 15% less transactivation activity and slightly reduced DNA binding; when associated with R-116; R-234; R-239; R-252 and R-262.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q06413-1.106.106", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q06413-1.110.110", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q06413-1.116.116", "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": "Q06413-1.234.234", "start_pos": 234, "end_pos": 234, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Myocyte enhancer factor 2 acetylation by p300 enhances its DNA binding activity, transcriptional activity, and myogenic differentiation.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Ma K, Chan JK, Zhu G, Wu Z", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "reference": [ { "type": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NGYGNPRNSPGLLVSPGNLN", "down_seq": "NMQAKSPPPMNLGMNNRKPD", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Reduced acetylation. Complete loss of acetylation, 15% less transactivation activity and slightly reduced DNA binding; when associated with R-116; R-119; R-239; R-252 and R-264.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q06413-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q06413-1.222.222", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q06413-1.228.228", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q06413-1.239.239", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q06413-1.240.240", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q06413-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q06413-1.252.252", "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": "Q06413-1.239.239", "start_pos": 239, "end_pos": 239, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Myocyte enhancer factor 2 acetylation by p300 enhances its DNA binding activity, transcriptional activity, and myogenic differentiation.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Ma K, Chan JK, Zhu G, Wu Z", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "reference": [ { "type": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PRNSPGLLVSPGNLNKNMQA", "down_seq": "SPPPMNLGMNNRKPDLRVLI", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Reduced acetylation. Complete loss of acetylation, 15% less transactivation activity and slightly reduced DNA binding; when associated with R-116; R-119; R-234; R-252 and R-264.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q06413-1.222.222", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q06413-1.228.228", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q06413-1.234.234", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q06413-1.240.240", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q06413-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q06413-1.252.252", "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": "Q06413-1.252.252", "start_pos": 252, "end_pos": 252, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Myocyte enhancer factor 2 acetylation by p300 enhances its DNA binding activity, transcriptional activity, and myogenic differentiation.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Ma K, Chan JK, Zhu G, Wu Z", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "reference": [ { "type": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LNKNMQAKSPPPMNLGMNNR", "down_seq": "PDLRVLIPPGSKNTMPSVSE", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Reduced acetylation. Complete loss of acetylation, 15% less transactivation activity and slightly reduced DNA binding; when associated with R-116; R-119; R-234; R-239 and R-264.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q06413-1.234.234", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q06413-1.239.239", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q06413-1.240.240", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q06413-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q06413-1.264.264", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q06413-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q06413-1.271.271", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q06413-1.272.272", "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": "Q06413-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Myocyte enhancer factor 2 acetylation by p300 enhances its DNA binding activity, transcriptional activity, and myogenic differentiation.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Ma K, Chan JK, Zhu G, Wu Z", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "reference": [ { "type": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MNLGMNNRKPDLRVLIPPGS", "down_seq": "NTMPSVSEDVDLLLNQRINN", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Reduced acetylation. Complete loss of acetylation, 15% less transactivation activity and slightly reduced DNA binding; when associated with R-116; R-119; R-234; R-239 and R-252.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15831463", "url": "https://glygen.org/publication/PubMed/15831463" } ] } ], "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "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 (KNT->NNT).", "chr_id": "5", "chr_pos": "88731747", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K264", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q06413-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q06413-1.252.252", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q06413-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q06413-1.271.271", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q06413-1.272.272", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q06413-1.273.273", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q06413-1.275.275", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Alternative pre-mRNA splicing governs expression of a conserved acidic transactivation domain in myocyte enhancer factor 2 factors of striated muscle and brain.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Zhu B, Ramachandran B, Gulick T", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "RefSeq", "id": "NP_001124477", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001124477" } ], "reference": [ { "type": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KPDLRVLIPPGSKNTMPSVS", "down_seq": "DVDLLLNQRINNSQSAQSLA", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "Q", "comment": "Reduced transcriptional activation. Completely abolishes transcriptional activation; when associated with N-273 and N-275.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q06413-1.252.252", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q06413-1.264.264", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q06413-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q06413-1.271.271", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q06413-1.273.273", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q06413-1.275.275", "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": "Q06413-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Alternative pre-mRNA splicing governs expression of a conserved acidic transactivation domain in myocyte enhancer factor 2 factors of striated muscle and brain.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Zhu B, Ramachandran B, Gulick T", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "RefSeq", "id": "NP_001124477", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001124477" } ], "reference": [ { "type": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PDLRVLIPPGSKNTMPSVSE", "down_seq": "VDLLLNQRINNSQSAQSLAT", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "N", "comment": "Reduced transcriptional activation. Completely abolishes transcriptional activation; when associated with Q-272 and N-275.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q06413-1.264.264", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q06413-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q06413-1.271.271", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q06413-1.272.272", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q06413-1.275.275", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q06413-1.293.293", "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": "Q06413-1.275.275", "start_pos": 275, "end_pos": 275, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Alternative pre-mRNA splicing governs expression of a conserved acidic transactivation domain in myocyte enhancer factor 2 factors of striated muscle and brain.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Zhu B, Ramachandran B, Gulick T", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "RefSeq", "id": "NP_001124477", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001124477" } ], "reference": [ { "type": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LRVLIPPGSKNTMPSVSEDV", "down_seq": "LLLNQRINNSQSAQSLATPV", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "N", "comment": "Reduced transcriptional activation. Completely abolishes transcriptional activation; when associated with Q-272 and N-273.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q06413-1.264.264", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q06413-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q06413-1.271.271", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q06413-1.272.272", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q06413-1.273.273", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q06413-1.293.293", "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": "Q06413-1.293.293", "start_pos": 293, "end_pos": 293, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Activation of the transcription factor MEF2C by the MAP kinase p38 in inflammation.", "journal": "Nature", "date": "1997", "authors": "Han J, Jiang Y, Li Z, Kravchenko VV, Ulevitch RJ", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "Reactome", "id": "R-HSA-525793", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-525793" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" } ] }, { "title": "BMK1/ERK5 regulates serum-induced early gene expression through transcription factor MEF2C.", "journal": "The EMBO journal", "date": "1997", "authors": "Kato Y, Kravchenko VV, Tapping RI, Han J, Ulevitch RJ, Lee JD", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ] }, { "title": "p38 and extracellular signal-regulated kinases regulate the myogenic program at multiple steps.", "journal": "Molecular and cellular biology", "date": "2000", "authors": "Wu Z, Woodring PJ, Bhakta KS, Tamura K, Wen F, Feramisco JR, Karin M, Wang JY, Puri PL", "evidence": [ { "database": "Reactome", "id": "R-HSA-525793", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-525793" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "10805738", "url": "https://glygen.org/publication/PubMed/10805738" } ] }, { "title": "Regulation of the MEF2 family of transcription factors by p38.", "journal": "Molecular and cellular biology", "date": "1999", "authors": "Zhao M, New L, Kravchenko VV, Kato Y, Gram H, di Padova F, Olson EN, Ulevitch RJ, Han J", "evidence": [ { "database": "Reactome", "id": "R-HSA-525793", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-525793" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "9858528", "url": "https://glygen.org/publication/PubMed/9858528" } ] }, { "title": "In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies.", "journal": "Molecular immunology", "date": "2020-07", "authors": "Pandey Kirti, Mifsud Nicole A, Lim Kam Sian Terry C C, Ayala Rochelle, Ternette Nicola, Ramarathinam Sri H, Purcell Anthony W", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "IEDB", "id": "458989", "url": "https://www.iedb.org/epitope/458989" }, { "database": "IEDB", "id": "885698", "url": "https://www.iedb.org/epitope/885698" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "10805738", "url": "https://glygen.org/publication/PubMed/10805738", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9858528", "url": "https://glygen.org/publication/PubMed/9858528", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://www.iedb.org/epitope/Q06413", "database": "IEDB", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q06413", "database": "PRO", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DVDLLLNQRINNSQSAQSLA", "down_seq": "PVVSVATPTLPGQGMGGYPS", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Abolishes MAPK14-mediated phosphorylation. No effect on MAPK7-mediated phosphorylation; when associated with A-300.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" }, { "database": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q16539-1", "kinase_gene_name": "MAPK14", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "10805738", "url": "https://glygen.org/publication/PubMed/10805738" }, { "database": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" }, { "database": "PubMed", "id": "9858528", "url": "https://glygen.org/publication/PubMed/9858528" } ], "site_lbl": "Thr293" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by MAPK14", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "IEDB", "id": "Q06413", "url": "https://www.iedb.org/epitope/Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" }, { "database": "PRO", "id": "Q06413", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q06413" }, { "database": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" }, { "database": "PubMed", "id": "10805738", "url": "https://glygen.org/publication/PubMed/10805738" }, { "database": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ], "site_lbl": "Thr293" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q06413-1.273.273", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q06413-1.275.275", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q06413-1.300.300", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Activation of the transcription factor MEF2C by the MAP kinase p38 in inflammation.", "journal": "Nature", "date": "1997", "authors": "Han J, Jiang Y, Li Z, Kravchenko VV, Ulevitch RJ", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "Reactome", "id": "R-HSA-525793", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-525793" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" } ] }, { "title": "BMK1/ERK5 regulates serum-induced early gene expression through transcription factor MEF2C.", "journal": "The EMBO journal", "date": "1997", "authors": "Kato Y, Kravchenko VV, Tapping RI, Han J, Ulevitch RJ, Lee JD", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ] }, { "title": "Regulation of the MEF2 family of transcription factors by p38.", "journal": "Molecular and cellular biology", "date": "1999", "authors": "Zhao M, New L, Kravchenko VV, Kato Y, Gram H, di Padova F, Olson EN, Ulevitch RJ, Han J", "evidence": [ { "database": "Reactome", "id": "R-HSA-525793", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-525793" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "9858528", "url": "https://glygen.org/publication/PubMed/9858528" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "9858528", "url": "https://glygen.org/publication/PubMed/9858528", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q06413", "database": "PRO", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QRINNSQSAQSLATPVVSVA", "down_seq": "PTLPGQGMGGYPSAISTTYG", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Abolishes MAPK14-mediated phosphorylation. No effect on MAPK7-mediated phosphorylation; when associated with A-293.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" }, { "database": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q16539-1", "kinase_gene_name": "MAPK14", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" }, { "database": "PubMed", "id": "9858528", "url": "https://glygen.org/publication/PubMed/9858528" } ], "site_lbl": "Thr300" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by MAPK14", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PRO", "id": "Q06413", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" }, { "database": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ], "site_lbl": "Thr300" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q06413-1.293.293", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.387.387", "start_pos": 387, "end_pos": 387, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Alternative pre-mRNA splicing governs expression of a conserved acidic transactivation domain in myocyte enhancer factor 2 factors of striated muscle and brain.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Zhu B, Ramachandran B, Gulick T", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "RefSeq", "id": "NP_001124477", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001124477" } ], "reference": [ { "type": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] }, { "title": "BMK1/ERK5 regulates serum-induced early gene expression through transcription factor MEF2C.", "journal": "The EMBO journal", "date": "1997", "authors": "Kato Y, Kravchenko VV, Tapping RI, Han J, Ulevitch RJ, Lee JD", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ] }, { "title": "Activation of the transcription factor MEF2C by the MAP kinase p38 in inflammation.", "journal": "Nature", "date": "1997", "authors": "Han J, Jiang Y, Li Z, Kravchenko VV, Ulevitch RJ", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "Reactome", "id": "R-HSA-525793", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-525793" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" } ] }, { "title": "Regulation of the MEF2 family of transcription factors by p38.", "journal": "Molecular and cellular biology", "date": "1999", "authors": "Zhao M, New L, Kravchenko VV, Kato Y, Gram H, di Padova F, Olson EN, Ulevitch RJ, Han J", "evidence": [ { "database": "Reactome", "id": "R-HSA-525793", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-525793" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "9858528", "url": "https://glygen.org/publication/PubMed/9858528" } ] }, { "title": "Brain-derived neurotrophic factor stimulates the transcriptional and neuroprotective activity of myocyte-enhancer factor 2C through an ERK1/2-RSK2 signaling cascade.", "journal": "Journal of neurochemistry", "date": "2007", "authors": "Wang Y, Liu L, Xia Z", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "17630987", "url": "https://glygen.org/publication/PubMed/17630987" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9858528", "url": "https://glygen.org/publication/PubMed/9858528", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17630987", "url": "https://glygen.org/publication/PubMed/17630987", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GACTSTHLSQSSNLSLPSTQ", "down_seq": "LNIKSEPVSPPRDRTTTPSR", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "No change in transactivational activation for isoforms with or without the beta domain.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q13164-1", "kinase_gene_name": "MAPK7", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ], "site_lbl": "Ser387" }, { "kinase_uniprot_canonical_ac": "Q16539-1", "kinase_gene_name": "MAPK14", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" }, { "database": "PubMed", "id": "9858528", "url": "https://glygen.org/publication/PubMed/9858528" } ], "site_lbl": "Ser387" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "17630987", "url": "https://glygen.org/publication/PubMed/17630987" } ], "site_lbl": "Ser387" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q06413-1.391.391", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q06413-1.396.396", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q06413-1.402.402", "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": 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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.391.391", "start_pos": 391, "end_pos": 391, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation-facilitated sumoylation of MEF2C negatively regulates its transcriptional activity.", "journal": "BMC biochemistry", "date": "2006", "authors": "Kang J, Gocke CB, Yu H", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "STHLSQSSNLSLPSTQSLNI", "down_seq": "SEPVSPPRDRTTTPSRYPQH", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Abolishes sumoylation.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q06413-1.387.387", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q06413-1.396.396", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q06413-1.402.402", "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": "Q06413-1.396.396", "start_pos": 396, "end_pos": 396, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation-facilitated sumoylation of MEF2C negatively regulates its transcriptional activity.", "journal": "BMC biochemistry", "date": "2006", "authors": "Kang J, Gocke CB, Yu H", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538" } ] }, { "title": "Alternative pre-mRNA splicing governs expression of a conserved acidic transactivation domain in myocyte enhancer factor 2 factors of striated muscle and brain.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Zhu B, Ramachandran B, Gulick T", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "RefSeq", "id": "NP_001124477", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001124477" } ], "reference": [ { "type": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" } ] }, { "title": "Phosphorylation and alternative pre-mRNA splicing converge to regulate myocyte enhancer factor 2C activity.", "journal": "Molecular and cellular biology", "date": "2004", "authors": "Zhu B, Gulick T", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "15340086", "url": "https://glygen.org/publication/PubMed/15340086" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15340086", "url": "https://glygen.org/publication/PubMed/15340086", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q06413", "database": "PRO", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QSSNLSLPSTQSLNIKSEPV", "down_seq": "PPRDRTTTPSRYPQHTRHEA", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Abolishes sumoylation. Enhanced transcriptional activity.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538" }, { "database": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" }, { "database": "PubMed", "id": "15340086", "url": "https://glygen.org/publication/PubMed/15340086" } ] }, { "sequence_org": "S", "sequence_mut": "A", "comment": "No change in transactivational activation for isoforms with or without the beta domain.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538" }, { "database": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" }, { "database": "PubMed", "id": "15340086", "url": "https://glygen.org/publication/PubMed/15340086" } ] }, { "sequence_org": "S", "sequence_mut": "C", "comment": "Abolishes sumoylation. Enhanced transcriptional activity.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538" }, { "database": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" }, { "database": "PubMed", "id": "15340086", "url": "https://glygen.org/publication/PubMed/15340086" } ] }, { "sequence_org": "S", "sequence_mut": "E", "comment": "No effect on sumoylation. No effect on transcriptional activity.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538" }, { "database": "PubMed", "id": "15834131", "url": "https://glygen.org/publication/PubMed/15834131" }, { "database": "PubMed", "id": "15340086", "url": "https://glygen.org/publication/PubMed/15340086" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06493-1", "kinase_gene_name": "CDK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538" } ], "site_lbl": "Ser396" }, { "kinase_uniprot_canonical_ac": "P14635-1", "kinase_gene_name": "CCNB1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538" } ], "site_lbl": "Ser396" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by CDK5", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "16478538", "url": "https://glygen.org/publication/PubMed/16478538" }, { "database": "PRO", "id": "Q06413", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q06413" }, { "database": "PubMed", "id": "15340086", "url": "https://glygen.org/publication/PubMed/15340086" } ], "site_lbl": "Ser396" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q06413-1.387.387", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q06413-1.391.391", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q06413-1.402.402", "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": 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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.419.419", "start_pos": 419, "end_pos": 419, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Activation of the transcription factor MEF2C by the MAP kinase p38 in inflammation.", "journal": "Nature", "date": "1997", "authors": "Han J, Jiang Y, Li Z, Kravchenko VV, Ulevitch RJ", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "Reactome", "id": "R-HSA-525793", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-525793" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" } ] }, { "title": "BMK1/ERK5 regulates serum-induced early gene expression through transcription factor MEF2C.", "journal": "The EMBO journal", "date": "1997", "authors": "Kato Y, Kravchenko VV, Tapping RI, Han J, Ulevitch RJ, Lee JD", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q06413", "database": "PRO", "categories": [ "Other" ] }, { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RDRTTTPSRYPQHTRHEAGR", "down_seq": "PVDSLSSCSSSYDGSDREDH", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "No effect on MAPK14-mediated phosphorylation. Abolishes MAPK7-mediated phosphorylation and reduces transactivation activity.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" }, { "database": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MAPK7", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PRO", "id": "Q06413", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "9069290", "url": "https://glygen.org/publication/PubMed/9069290" }, { "database": "PubMed", "id": "9384584", "url": "https://glygen.org/publication/PubMed/9384584" } ], "site_lbl": "Ser419" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q06413-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q06413-1.423.423", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q06413-1.425.425", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q06413-1.432.432", "categories": [ "mutagenesis_flag", "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": 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": "Q06413-1.432.432", "start_pos": 432, "end_pos": 432, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Dominant-interfering forms of MEF2 generated by caspase cleavage contribute to NMDA-induced neuronal apoptosis.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2002", "authors": "Okamoto S, Li Z, Ju C, Scholzke MN, Mathews E, Cui J, Salvesen GS, Bossy-Wetzel E, Lipton SA", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "reference": [ { "type": "PubMed", "id": "11904443", "url": "https://glygen.org/publication/PubMed/11904443" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11904443", "url": "https://glygen.org/publication/PubMed/11904443", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TRHEAGRSPVDSLSSCSSSY", "down_seq": "GSDREDHRNEFHSPIGLTRP", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolishes cleavage by caspase 7.", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "11904443", "url": "https://glygen.org/publication/PubMed/11904443" } ] } ], "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "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 (DGS->NGS).", "chr_id": "5", "chr_pos": "88722732", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D432", "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": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q06413-1.419.419", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q06413-1.423.423", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q06413-1.425.425", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q06413-1.442.442", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q06413-1.445.445", "categories": [ "phosphorylation_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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ETLRKKGLNGCDSPDPDADD", "down_seq": "VGHSPESEDKYRKINEDIDL", "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "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: num. of cancers (3).", "chr_id": "5", "chr_pos": "88761270", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S106", "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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "site_lbl": "Ser106" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q06413-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q06413-1.110.110", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q06413-1.116.116", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q06413-1.119.119", "categories": [ "mutagenesis_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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_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": "Q06413-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1370166849", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1370166849", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1370166849", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1370166849", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "RLCAVPPPNFEMPVSIPVSS", "down_seq": "NSLVYSNPVSSLGNPNLLPL", "snv": [ { "evidence": [ { "id": "rs1370166849", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1370166849" }, { "id": "rs1370166849", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1370166849" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HNS->NNS).", "chr_id": "5", "chr_pos": "88751992", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H152", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q06413-1.150.150", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q06413-1.151.151", "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": "Q06413-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GNPNLLPLAHPSLQRNSMSP", "down_seq": "VTHRPPSAGNTGGLMGGDLT", "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "5", "chr_pos": "88751893", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "G185", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q06413-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q06413-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q06413-1.192.192", "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": 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": "Q06413-1.189.189", "start_pos": 189, "end_pos": 189, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LLPLAHPSLQRNSMSPGVTH", "down_seq": "PPSAGNTGGLMGGDLTSGAG", "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "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": "5", "chr_pos": "88751880", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R189", "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: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": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q06413-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q06413-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q06413-1.192.192", "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": "Q06413-1.216.216", "start_pos": 216, "end_pos": 216, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1761824693", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1761824693", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1761824693", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1761824693", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TGGLMGGDLTSGAGTSAGNG", "down_seq": "GNPRNSPGLLVSPGNLNKNM", "snv": [ { "evidence": [ { "id": "rs1761824693", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1761824693" }, { "id": "rs1761824693", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1761824693" } ], "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 (NGY->NGC).", "chr_id": "5", "chr_pos": "88731892", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y216", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q06413-1.222.222", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q06413-1.228.228", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q06413-1.234.234", "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": "Q06413-1.251.251", "start_pos": 251, "end_pos": 251, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1761787183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1761787183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1761787183", "url": "https://www.ensembl.org/id/rs1761787183", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NLNKNMQAKSPPPMNLGMNN", "down_seq": "KPDLRVLIPPGSKNTMPSVS", "snv": [ { "evidence": [ { "id": "rs1761787183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1761787183" }, { "id": "rs1761787183", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1761787183" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNR->NNC).", "chr_id": "5", "chr_pos": "88731788", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R251", "disease": [ { "disease_id": "DOID:0070050", "recommended_name": { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "An autosomal dominant intellectual developmental disorder that is characterized by global developmental delay with hypotonia, poor motor development with limited walking, impaired intellectual development with poor or absent speech, and behavioral abnormalities and that has_material_basis_in an autosomal dominant mutation of the MEF2C gene on chromosome 5q14.3." }, "synonyms": [ { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "MRD20", "description": "" }, { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "mental retardation, autosomal dominant 20", "description": "" }, { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "autosomal dominant mental retardation 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "Any autosomal dominant non-syndromic intellectual disability in which the cause of the disease is a mutation in the MEF2C gene." }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C Deficiency", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C autosomal dominant non-syndromic intellectual disability", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C haploinsufficiency syndrome (MCHS)", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C-related neurodevelopmental disorder", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C-related syndrome", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MRD20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "autosomal dominant non-syndromic intellectual disability caused by mutation in MEF2C", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "intellectual disability, autosomal dominant 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "intellectual disability, autosomal dominant type 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, autosomal dominant 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, autosomal dominant type 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, stereotypic movements, epilepsy, and/or cerebral malformations", "description": "" }, { "id": "MIM:613443", "resource": "MIM", "url": "https://www.omim.org/entry/613443", "name": "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language" } ], "unlinked_id_list": [], "evidence": [ { "id": "613443", "database": "MIM", "url": "https://www.omim.org/entry/613443" }, { "id": "0070050", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0070050" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNR->NNS).", "chr_id": "5", "chr_pos": "88731788", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R251", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q06413-1.234.234", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q06413-1.239.239", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q06413-1.240.240", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q06413-1.252.252", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q06413-1.264.264", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q06413-1.267.267", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q06413-1.271.271", "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": 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": "Q06413-1.267.267", "start_pos": 267, "end_pos": 267, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1561697163", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1561697163", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1561697163", "url": "https://www.ensembl.org/id/rs1561697163", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "GMNNRKPDLRVLIPPGSKNT", "down_seq": "PSVSEDVDLLLNQRINNSQS", "snv": [ { "evidence": [ { "id": "rs1561697163", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1561697163" }, { "id": "rs1561697163", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1561697163" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTM->NTT).", "chr_id": "5", "chr_pos": "88731739", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M267", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q06413-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q06413-1.252.252", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q06413-1.264.264", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q06413-1.271.271", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q06413-1.272.272", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q06413-1.273.273", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q06413-1.275.275", "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": "Q06413-1.339.339", "start_pos": 339, "end_pos": 339, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs797045703", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs797045703", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs797045703", "url": "https://www.ncbi.nlm.nih.gov/snp/rs797045703#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs797045703", "url": "http://gnomad.broadinstitute.org/awesome?query=rs797045703", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs778783316", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778783316", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778783316", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778783316", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778783316", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778783316#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778783316", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778783316", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "YGTEYSLSSADLSSLSGFNT", "down_seq": "SALHLGSVTGWQQQHLHNMP", "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" }, { "id": "rs797045703", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs797045703" }, { "id": "rs797045703", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs797045703#frequency_tab" }, { "id": "rs797045703", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs797045703" }, { "id": "rs778783316", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778783316" }, { "id": "rs778783316", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778783316" }, { "id": "rs778783316", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778783316#frequency_tab" }, { "id": "rs778783316", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778783316" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTT).", "chr_id": "5", "chr_pos": "88728578", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A339", "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:0070050", "recommended_name": { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "An autosomal dominant intellectual developmental disorder that is characterized by global developmental delay with hypotonia, poor motor development with limited walking, impaired intellectual development with poor or absent speech, and behavioral abnormalities and that has_material_basis_in an autosomal dominant mutation of the MEF2C gene on chromosome 5q14.3." }, "synonyms": [ { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "MRD20", "description": "" }, { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "mental retardation, autosomal dominant 20", "description": "" }, { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "autosomal dominant mental retardation 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "Any autosomal dominant non-syndromic intellectual disability in which the cause of the disease is a mutation in the MEF2C gene." }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C Deficiency", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C autosomal dominant non-syndromic intellectual disability", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C haploinsufficiency syndrome (MCHS)", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C-related neurodevelopmental disorder", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C-related syndrome", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MRD20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "autosomal dominant non-syndromic intellectual disability caused by mutation in MEF2C", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "intellectual disability, autosomal dominant 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "intellectual disability, autosomal dominant type 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, autosomal dominant 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, autosomal dominant type 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, stereotypic movements, epilepsy, and/or cerebral malformations", "description": "" }, { "id": "MIM:613443", "resource": "MIM", "url": "https://www.omim.org/entry/613443", "name": "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language" } ], "unlinked_id_list": [], "evidence": [ { "id": "613443", "database": "MIM", "url": "https://www.omim.org/entry/613443" }, { "id": "0070050", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0070050" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q06413-1.359.359", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "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": "Q06413-1.359.359", "start_pos": 359, "end_pos": 359, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1355343472", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1355343472", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1355343472", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1355343472#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1355343472", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1355343472", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ASALHLGSVTGWQQQHLHNM", "down_seq": "PSALSQLGACTSTHLSQSSN", "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NMP->NMS).", "chr_id": "5", "chr_pos": "88728518", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P359", "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": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" }, { "id": "rs1355343472", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1355343472" }, { "id": "rs1355343472", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1355343472#frequency_tab" }, { "id": "rs1355343472", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1355343472" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NMP->NMT).", "chr_id": "5", "chr_pos": "88728518", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P359", "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", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q06413-1.339.339", "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": 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": "Q06413-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1756812909", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1756812909", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1756812909", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1756812909", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LPSTQSLNIKSEPVSPPRDR", "down_seq": "TTPSRYPQHTRHEAGRSPVD", "snv": [ { "evidence": [ { "id": "rs1756812909", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1756812909" }, { "id": "rs1756812909", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1756812909" } ], "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": "5", "chr_pos": "88722815", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T402", "disease": [ { "disease_id": "DOID:0070050", "recommended_name": { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "An autosomal dominant intellectual developmental disorder that is characterized by global developmental delay with hypotonia, poor motor development with limited walking, impaired intellectual development with poor or absent speech, and behavioral abnormalities and that has_material_basis_in an autosomal dominant mutation of the MEF2C gene on chromosome 5q14.3." }, "synonyms": [ { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "MRD20", "description": "" }, { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "mental retardation, autosomal dominant 20", "description": "" }, { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "autosomal dominant mental retardation 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "Any autosomal dominant non-syndromic intellectual disability in which the cause of the disease is a mutation in the MEF2C gene." }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C Deficiency", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C autosomal dominant non-syndromic intellectual disability", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C haploinsufficiency syndrome (MCHS)", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C-related neurodevelopmental disorder", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C-related syndrome", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MRD20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "autosomal dominant non-syndromic intellectual disability caused by mutation in MEF2C", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "intellectual disability, autosomal dominant 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "intellectual disability, autosomal dominant type 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, autosomal dominant 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, autosomal dominant type 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, stereotypic movements, epilepsy, and/or cerebral malformations", "description": "" }, { "id": "MIM:613443", "resource": "MIM", "url": "https://www.omim.org/entry/613443", "name": "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language" } ], "unlinked_id_list": [], "evidence": [ { "id": "613443", "database": "MIM", "url": "https://www.omim.org/entry/613443" }, { "id": "0070050", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0070050" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q06413-1.387.387", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q06413-1.391.391", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q06413-1.396.396", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q06413-1.419.419", "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": [ "sequence_org", "sequence_mut", "comment", "chr_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": "Q06413-1.423.423", "start_pos": 423, "end_pos": 423, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1756781755", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1756781755", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1756781755", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1756781755#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1345666452", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1345666452", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1345666452", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1345666452#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TTPSRYPQHTRHEAGRSPVD", "down_seq": "LSSCSSSYDGSDREDHRNEF", "snv": [ { "evidence": [ { "id": "rs1756781755", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1756781755" }, { "id": "rs1756781755", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1756781755#frequency_tab" }, { "id": "rs1345666452", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1345666452" }, { "id": "rs1345666452", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1345666452#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 (SLS->NLS).", "chr_id": "5", "chr_pos": "88722752", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S423", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0070050", "recommended_name": { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "An autosomal dominant intellectual developmental disorder that is characterized by global developmental delay with hypotonia, poor motor development with limited walking, impaired intellectual development with poor or absent speech, and behavioral abnormalities and that has_material_basis_in an autosomal dominant mutation of the MEF2C gene on chromosome 5q14.3." }, "synonyms": [ { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "MRD20", "description": "" }, { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "mental retardation, autosomal dominant 20", "description": "" }, { "id": "DOID:0070050", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0070050", "name": "autosomal dominant mental retardation 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "Any autosomal dominant non-syndromic intellectual disability in which the cause of the disease is a mutation in the MEF2C gene." }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C Deficiency", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C autosomal dominant non-syndromic intellectual disability", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C haploinsufficiency syndrome (MCHS)", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C-related neurodevelopmental disorder", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MEF2C-related syndrome", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "MRD20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "autosomal dominant non-syndromic intellectual disability caused by mutation in MEF2C", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "intellectual disability, autosomal dominant 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "intellectual disability, autosomal dominant type 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, autosomal dominant 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, autosomal dominant type 20", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "" }, { "id": "MONDO:0013266", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013266", "name": "mental retardation, stereotypic movements, epilepsy, and/or cerebral malformations", "description": "" }, { "id": "MIM:613443", "resource": "MIM", "url": "https://www.omim.org/entry/613443", "name": "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language", "description": "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language" } ], "unlinked_id_list": [], "evidence": [ { "id": "613443", "database": "MIM", "url": "https://www.omim.org/entry/613443" }, { "id": "0070050", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0070050" } ] } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q06413-1.419.419", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q06413-1.425.425", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q06413-1.432.432", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q06413-1.442.442", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_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": "Q06413-1.425.425", "start_pos": 425, "end_pos": 425, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1756781755", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1756781755", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1756781755", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1756781755#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSRYPQHTRHEAGRSPVDSL", "down_seq": "SCSSSYDGSDREDHRNEFHS", "snv": [ { "evidence": [ { "id": "rs1756781755", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1756781755" }, { "id": "rs1756781755", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1756781755#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 (SSC->NSC).", "chr_id": "5", "chr_pos": "88722752", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S425", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q06413-1.419.419", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q06413-1.423.423", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q06413-1.432.432", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q06413-1.442.442", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q06413-1.445.445", "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": "Q06413-1.442.442", "start_pos": 442, "end_pos": 442, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DSLSSCSSSYDGSDREDHRN", "down_seq": "FHSPIGLTRPSPDERESPSV", "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "88722702", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E442", "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: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": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q06413-1.423.423", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q06413-1.425.425", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q06413-1.432.432", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q06413-1.445.445", "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": "Q06413-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RKFGLMKKAYELSVLCDCEI", "down_seq": "LIIFNSTNKLFQYASTDMDK", "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "88804725", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A44", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q06413-1.59.59", "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": "Q06413-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "FQYASTDMDKVLLKYTEYNE", "down_seq": "HESRTNSDIVETLRKKGLNG", "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NEP->NES).", "chr_id": "5", "chr_pos": "88804633", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P75", "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": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q06413-1.59.59", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q06413-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q06413-1.80.80", "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": "Q06413-1.76.76", "start_pos": 76, "end_pos": 76, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "QYASTDMDKVLLKYTEYNEP", "down_seq": "ESRTNSDIVETLRKKGLNGC", "snv": [ { "evidence": [ { "id": "Q06413", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06413" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "H", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "5", "chr_pos": "88804629", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H76", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q06413-1.59.59", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q06413-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q06413-1.80.80", "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": 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": "Q06413-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKGLNGCDSPDPDADDSVGH", "down_seq": "PESEDKYRKINEDIDLMISR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "site_lbl": "Ser110" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q06413-1.98.98", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q06413-1.106.106", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q06413-1.116.116", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q06413-1.119.119", "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": 0 } ], "sort_fields": [] } ] }, { "id": "Q06413-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry.", "journal": "Nature communications", "date": "2016-11-21", "authors": "Bassani-Sternberg Michal, Br\u00e4unlein Eva, Klar Richard, Engleitner Thomas, Sinitcyn Pavel, Audehm Stefan, Straub Melanie, Weber Julia, Slotta-Huspenina Julia, Specht Katja, Martignoni Marc E, Werner Angelika, Hein R\u00fcdiger, H Busch Dirk, Peschel Christian, Rad Roland, Cox J\u00fcrgen, Mann Matthias, Krackhardt Angela M", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121" } ] }, { "title": "Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands.", "journal": "Molecular & cellular proteomics : MCP", "date": "2020-02", "authors": "Solleder Marthe, Guillaume Philippe, Racle Julien, Michaux Justine, Pak Hui-Song, M\u00fcller Markus, Coukos George, Bassani-Sternberg Michal, Gfeller David", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "IEDB", "id": "705928", "url": "https://www.iedb.org/epitope/705928" }, { "database": "IEDB", "id": "728507", "url": "https://www.iedb.org/epitope/728507" }, { "database": "IEDB", "id": "885698", "url": "https://www.iedb.org/epitope/885698" } ], "reference": [ { "type": "PubMed", "id": "31848261", "url": "https://glygen.org/publication/PubMed/31848261" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.iedb.org/epitope/Q06413", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31848261", "url": "https://glygen.org/publication/PubMed/31848261", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLGNPNLLPLAHPSLQRNSM", "down_seq": "PGVTHRPPSAGNTGGLMGGD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q06413", "url": "https://www.iedb.org/epitope/Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121" }, { "database": "PubMed", "id": "31848261", "url": "https://glygen.org/publication/PubMed/31848261" } ], "site_lbl": "Ser183" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q06413-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q06413-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q06413-1.192.192", "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": "Q06413-1.192.192", "start_pos": 192, "end_pos": 192, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Brain-derived neurotrophic factor stimulates the transcriptional and neuroprotective activity of myocyte-enhancer factor 2C through an ERK1/2-RSK2 signaling cascade.", "journal": "Journal of neurochemistry", "date": "2007", "authors": "Wang Y, Liu L, Xia Z", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "17630987", "url": "https://glygen.org/publication/PubMed/17630987" } ] } ], "crossref": [ { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17630987", "url": "https://glygen.org/publication/PubMed/17630987", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAHPSLQRNSMSPGVTHRPP", "down_seq": "AGNTGGLMGGDLTSGAGTSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P51812-1", "kinase_gene_name": "RPS6KA3", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "17630987", "url": "https://glygen.org/publication/PubMed/17630987" } ], "site_lbl": "Ser192" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q06413-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q06413-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q06413-1.189.189", "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": "Q06413-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Regulation of neuroprotective activity of myocyte-enhancer factor 2 by cAMP-protein kinase A signaling pathway in neuronal survival.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Wang X, Tang X, Li M, Marshall J, Mao Z", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "15735306", "url": "https://glygen.org/publication/PubMed/15735306" } ] } ], "crossref": [ { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15735306", "url": "https://glygen.org/publication/PubMed/15735306", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "", "down_seq": "FTKRKFGLMKKAYELSVLCD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "15735306", "url": "https://glygen.org/publication/PubMed/15735306" } ], "site_lbl": "Thr20" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "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": "Q06413-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "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": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AGTSAGNGYGNPRNSPGLLV", "down_seq": "PGNLNKNMQAKSPPPMNLGM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "site_lbl": "Ser228" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q06413-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q06413-1.222.222", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q06413-1.234.234", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q06413-1.239.239", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q06413-1.240.240", "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": "Q06413-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "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": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "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": "RNSPGLLVSPGNLNKNMQAK", "down_seq": "PPPMNLGMNNRKPDLRVLIP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser240" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q06413-1.222.222", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q06413-1.228.228", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q06413-1.234.234", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q06413-1.239.239", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q06413-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q06413-1.252.252", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.445.445", "start_pos": 445, "end_pos": 445, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "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": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens.", "journal": "Molecular & cellular proteomics : MCP", "date": "2017-02", "authors": "Alp\u00edzar Ad\u00e1n, Marino Fabio, Ramos-Fern\u00e1ndez Antonio, Lombard\u00eda Manuel, Jeko Anita, Pazos Florencio, Paradela Alberto, Santiago C\u00e9sar, Heck Albert J R, Marcilla Miguel", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "IEDB", "id": "223443", "url": "https://www.iedb.org/epitope/223443" } ], "reference": [ { "type": "PubMed", "id": "27920218", "url": "https://glygen.org/publication/PubMed/27920218" } ] } ], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://www.iedb.org/epitope/Q06413", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "27920218", "url": "https://glygen.org/publication/PubMed/27920218", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSCSSSYDGSDREDHRNEFH", "down_seq": "PIGLTRPSPDERESPSVKRM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "IEDB", "id": "Q06413", "url": "https://www.iedb.org/epitope/Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "27920218", "url": "https://glygen.org/publication/PubMed/27920218" } ], "site_lbl": "Ser445" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q06413-1.425.425", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q06413-1.432.432", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q06413-1.442.442", "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": "Q06413-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of the MADS-Box transcription factor MEF2C enhances its DNA binding activity.", "journal": "The Journal of biological chemistry", "date": "1996", "authors": "Molkentin JD, Li L, Olson EN", "evidence": [ { "database": "iPTMnet", "id": "Q06413-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413-1" } ], "reference": [ { "type": "PubMed", "id": "8663403", "url": "https://glygen.org/publication/PubMed/8663403" } ] } ], "crossref": [ { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "8663403", "url": "https://glygen.org/publication/PubMed/8663403", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CDCEIALIIFNSTNKLFQYA", "down_seq": "TDMDKVLLKYTEYNEPHESR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P68400-1", "kinase_gene_name": "CSNK2A1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "8663403", "url": "https://glygen.org/publication/PubMed/8663403" } ], "site_lbl": "Ser59" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by CK2", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "8663403", "url": "https://glygen.org/publication/PubMed/8663403" } ], "site_lbl": "Ser59" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q06413-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q06413-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q06413-1.76.76", "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": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Skeletal myosin light chain kinase regulates skeletal myogenesis by phosphorylation of MEF2C.", "journal": "The EMBO journal", "date": "2011", "authors": "Al Madhoun AS, Mehta V, Li G, Figeys D, Wiper-Bergeron N, Skerjanc IS", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" } ], "reference": [ { "type": "PubMed", "id": "21556048", "url": "https://glygen.org/publication/PubMed/21556048" } ] } ], "crossref": [ { "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21556048", "url": "https://glygen.org/publication/PubMed/21556048", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06413", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q06413*", "database": "IntAct", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TDMDKVLLKYTEYNEPHESR", "down_seq": "NSDIVETLRKKGLNGCDSPD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q32MK0-3", "kinase_gene_name": "MYLK3", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "21556048", "url": "https://glygen.org/publication/PubMed/21556048" } ], "site_lbl": "Thr80" }, { "kinase_uniprot_canonical_ac": "Q9H1R3-1", "kinase_gene_name": "MYLK2", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "21556048", "url": "https://glygen.org/publication/PubMed/21556048" } ], "site_lbl": "Thr80" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IntAct", "id": "Q06413", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q06413*" }, { "database": "iPTMnet", "id": "Q06413", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06413" }, { "database": "PubMed", "id": "21556048", "url": "https://glygen.org/publication/PubMed/21556048" } ], "site_lbl": "Thr80" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q06413-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q06413-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q06413-1.98.98", "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": 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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06413-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "Q06413-1", "length": 473, "uniprot_id": "MEF2C_HUMAN", "protein_name": "Myocyte-specific enhancer factor 2C", "refseq_ac": "NP_001124477", "refseq_name": "myocyte-specific enhancer factor 2C isoform 2", "gene_name": "MEF2C", "gene_names_uniprotkb": "MEF2C", "gene_names_refseq": "C5DELq14.3; DEL5q14.3; MEF2C; NEDHSIL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRTNSDIVETLRKKGLNGCD", "down_seq": "PDPDADDSVGHSPESEDKYR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q06413", "url": "https://www.uniprot.org/uniprotkb/Q06413" } ], "site_lbl": "Ser98" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "271", "end_pos": "271" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "98", "end_pos": "98" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q06413-1.80.80", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q06413-1.106.106", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q06413-1.110.110", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q06413-1.116.116", "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": 0 } ], "sort_fields": [] } ] }, { "id": "P53582-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P53582-1", "length": 386, "uniprot_id": "MAP11_HUMAN", "protein_name": "Methionine aminopeptidase 1", "refseq_ac": "NP_055958", "refseq_name": "methionine aminopeptidase 1", "gene_name": "METAP1", "gene_names_uniprotkb": "METAP1; KIAA0094", "gene_names_refseq": "MAP1A; METAP1; MetAP1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P53582", "url": "https://www.uniprot.org/uniprotkb/P53582" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P53582", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P53582" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P53582", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P53582" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "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": "P53582", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P53582" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Synthesis of Na2S2O4 mediated cleavable affinity tag for labeling of O-GlcNAc modified proteins via azide-alkyne cycloaddition.", "journal": "Bioorganic & medicinal chemistry letters", "date": "2021", "authors": "Wang J, Dou B, Zheng L, Cao W, Zeng X, Wen Y, Ma J, Li X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P53582", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P53582" } ], "reference": [ { "type": "PubMed", "id": "34229054", "url": "https://glygen.org/publication/PubMed/34229054" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P53582", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P53582" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P53582", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P53582", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34229054", "url": "https://glygen.org/publication/PubMed/34229054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "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": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "P53582", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P53582" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "34229054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34229054" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "334", "end_pos": "334" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "253", "end_pos": "253" } ] } ], "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] } ]